Upload folder using huggingface_hub (part 2)

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/cmake/FindSuperLU.cmake

@@ -0,0 +1,103 @@
+################################################################################
+# [FETK header]
+# From eigen/cmake/FindSuperLU.cmake
+# https://gitlab.com/libeigen/eigen/-/blob/master/cmake/FindSuperLU.cmake
+# Accessed on June 18, 2021
+################################################################################
+
+# Umfpack lib usually requires linking to a blas library.
+# It is up to the user of this module to find a BLAS and link to it.
+
+if (SUPERLU_INCLUDES AND SUPERLU_LIBRARIES)
+  set(SUPERLU_FIND_QUIETLY TRUE)
+endif ()
+
+find_path(SUPERLU_INCLUDES
+  NAMES
+  supermatrix.h
+  PATHS
+  $ENV{SUPERLUDIR}
+  ${INCLUDE_INSTALL_DIR}
+  PATH_SUFFIXES
+  superlu
+  SRC
+)
+
+find_library(SUPERLU_LIBRARIES
+  NAMES "superlu_5.2.1" "superlu_5.2" "superlu_5.1.1" "superlu_5.1" "superlu_5.0" "superlu_4.3" "superlu_4.2" "superlu_4.1" "superlu_4.0" "superlu_3.1" "superlu_3.0" "superlu"
+  PATHS $ENV{SUPERLUDIR} ${LIB_INSTALL_DIR}
+  PATH_SUFFIXES lib)
+
+if(SUPERLU_INCLUDES AND SUPERLU_LIBRARIES)
+
+include(CheckCXXSourceCompiles)
+include(CMakePushCheckState)
+cmake_push_check_state()
+
+set(CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${SUPERLU_INCLUDES})
+
+# check whether struct mem_usage_t is globally defined
+check_cxx_source_compiles("
+typedef int int_t;
+#include <supermatrix.h>
+#include <slu_util.h>
+int main() {
+  mem_usage_t mem;
+  return 0;
+}"
+SUPERLU_HAS_GLOBAL_MEM_USAGE_T)
+
+
+check_cxx_source_compiles("
+typedef int int_t;
+#include <supermatrix.h>
+#include <superlu_enum_consts.h>
+int main() {
+  return SLU_SINGLE;
+}"
+SUPERLU_HAS_CLEAN_ENUMS)
+
+check_cxx_source_compiles("
+typedef int int_t;
+#include <supermatrix.h>
+#include <slu_util.h>
+int main(void)
+{
+  GlobalLU_t glu;
+  return 0;
+}"
+SUPERLU_HAS_GLOBALLU_T)
+
+if(SUPERLU_HAS_GLOBALLU_T)
+  # at least 5.0
+  set(SUPERLU_VERSION_VAR "5.0")
+elseif(SUPERLU_HAS_CLEAN_ENUMS)
+  # at least 4.3
+  set(SUPERLU_VERSION_VAR "4.3")
+elseif(SUPERLU_HAS_GLOBAL_MEM_USAGE_T)
+  # at least 4.0
+  set(SUPERLU_VERSION_VAR "4.0")
+else()
+  set(SUPERLU_VERSION_VAR "3.0")
+endif()
+
+cmake_pop_check_state()
+
+if(SuperLU_FIND_VERSION)
+  if(${SUPERLU_VERSION_VAR} VERSION_LESS ${SuperLU_FIND_VERSION})
+    set(SUPERLU_VERSION_OK FALSE)
+  else()
+    set(SUPERLU_VERSION_OK TRUE)
+  endif()
+else()
+  set(SUPERLU_VERSION_OK TRUE)
+endif()
+
+endif()
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(SuperLU
+                                  REQUIRED_VARS SUPERLU_INCLUDES SUPERLU_LIBRARIES SUPERLU_VERSION_OK
+                                  VERSION_VAR SUPERLU_VERSION_VAR)
+
+mark_as_advanced(SUPERLU_INCLUDES SUPERLU_LIBRARIES)

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/cmake/FindUMFPACK.cmake

@@ -0,0 +1,39 @@
+################################################################################
+# [FETK header]
+# From eigen/cmake/FindUMFPACK.cmake
+# https://gitlab.com/libeigen/eigen/-/blob/master/cmake/FindUMFPACK.cmake
+# Accessed on June 18, 2021
+################################################################################
+
+# Umfpack lib usually requires linking to a blas library.
+# It is up to the user of this module to find a BLAS and link to it.
+
+if (UMFPACK_INCLUDES AND UMFPACK_LIBRARIES)
+  set(UMFPACK_FIND_QUIETLY TRUE)
+endif ()
+
+find_path(UMFPACK_INCLUDES
+  NAMES
+  umfpack.h
+  PATHS
+  $ENV{UMFPACKDIR}
+  ${INCLUDE_INSTALL_DIR}
+  PATH_SUFFIXES
+  suitesparse
+  ufsparse
+)
+
+find_library(UMFPACK_LIBRARIES 
+  NAMES umfpack libumfpack 
+  PATHS $ENV{UMFPACKDIR} ${LIB_INSTALL_DIR}
+)
+
+if(UMFPACK_LIBRARIES AND NOT UMFPACK_LIBDIR)
+    get_filename_component(UMFPACK_LIBDIR ${UMFPACK_LIBRARIES} PATH)
+endif()
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(UMFPACK DEFAULT_MSG
+                                  UMFPACK_INCLUDES UMFPACK_LIBRARIES UMFPACK_LIBDIR)
+
+mark_as_advanced(UMFPACK_INCLUDES UMFPACK_LIBRARIES UMFPACK_LIBDIR)

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/1d7h-dmso-mol.in

@@ -0,0 +1,287 @@
+##########################################################################
+# 1D7H/DMSO BINDING ENERGY
+##########################################################################
+
+read 
+  mol pqr 1d7h-dmso-complex.pqr
+  mol pqr dmso-min.pqr
+  mol pqr 1d7h-min.pqr 
+end
+
+# COMPLEX -- SOLVATED STATE (FOCUSING)
+elec name complex-solv-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 1
+    mol 1
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name complex-solv-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 1
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# COMPLEX -- REFERENCE STATE (FOCUSING)
+elec name complex-ref-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 1
+    mol 1
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name complex-ref-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 1
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# DMSO -- SOLVATED STATE (FOCUSING)
+elec name dmso-solv-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name dmso-solv-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# DMSO -- REFERENCE STATE (FOCUSING)
+elec name dmso-ref-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name dmso-ref-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# 1D7H -- SOLVATED STATE (FOCUSING)
+elec name 1d7h-solv-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 3
+    mol 3
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name 1d7h-solv-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 3
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# 1D7H -- REFERENCE STATE (FOCUSING)
+elec name 1d7h-ref-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 3
+    mol 3
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name 1d7h-ref-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 3
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# COMPLEX SOLVATION ENERGY
+print elecEnergy complex-solv-fine - complex-ref-fine end
+
+# DMSO SOLVATION ENERGY
+print elecEnergy dmso-solv-fine - dmso-ref-fine end
+
+# 1D7H SOLVATION ENERGY
+print elecEnergy 1d7h-solv-fine - 1d7h-ref-fine end
+
+# CHANGE IN SOLVATION ENERGY UPON BINDING
+print elecEnergy complex-solv-fine - complex-ref-fine - dmso-solv-fine + dmso-ref-fine - 1d7h-solv-fine + 1d7h-ref-fine end
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/1d7h-dmso-mol.out

@@ -0,0 +1,449 @@
+
+
+----------------------------------------------------------------------
+    APBS -- Adaptive Poisson-Boltzmann Solver
+    Version APBS 3.4.1
+    
+    Nathan A. Baker (nathan.baker@pnnl.gov)
+    Pacific Northwest National Laboratory
+    
+    Additional contributing authors listed in the code documentation.
+    
+    Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
+    Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
+    Northwest Division for the U.S. Department of Energy.
+    
+    Portions Copyright (c) 2002-2010, Washington University in St. Louis.
+    Portions Copyright (c) 2002-2020, Nathan A. Baker.
+    Portions Copyright (c) 1999-2002, The Regents of the University of California.
+    Portions Copyright (c) 1995, Michael Holst.
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+    
+    * Redistributions of source code must retain the above copyright notice, this
+      list of conditions and the following disclaimer.
+    
+    * Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+    
+    * Neither the name of the developer nor the names of its contributors may be
+      used to endorse or promote products derived from this software without
+      specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+    ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+    ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+    (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+    LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+    ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+----------------------------------------------------------------------
+    APBS uses FETK (the Finite Element ToolKit) to solve the
+    Poisson-Boltzmann equation numerically.  FETK is a portable collection
+    of finite element modeling class libraries developed by the Michael Holst
+    research group and written in an object-oriented form of C.  FEtk is
+    designed to solve general coupled systems of nonlinear partial differential
+    equations using adaptive finite element methods, inexact Newton methods,
+    and algebraic multilevel methods.  More information about FEtk may be found
+    at <http://www.FEtk.ORG>.
+----------------------------------------------------------------------
+    APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
+    Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
+    which has been modified by Patrice Koehl
+    <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
+    memory usage when solving the Poisson-Boltzmann equation.
+----------------------------------------------------------------------
+    Please cite your use of APBS as:
+
+    Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
+    nanosystems: application to microtubules and the ribosome. Proc.
+    Natl. Acad. Sci. USA 98, 10037-10041 2001.
+    
+
+This executable compiled on Apr 29 2022 at 19:42:46
+
+Parsing input file 1d7h-dmso-mol.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from 1d7h-dmso-complex.pqr.
+  1673 atoms
+  Centered at (2.587e+01, 1.835e+01, 1.911e+01)
+  Net charge 9.91e-01 e
+Reading PQR-format atom data from dmso-min.pqr.
+  10 atoms
+  Centered at (1.775e+01, 1.777e+01, 2.049e+01)
+  Net charge 2.78e-17 e
+Reading PQR-format atom data from 1d7h-min.pqr.
+  1663 atoms
+  Centered at (2.587e+01, 1.835e+01, 1.911e+01)
+  Net charge 9.91e-01 e
+Preparing to run 12 PBE calculations.
+----------------------------------------
+CALCULATION #1 (complex-solv-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  122.059 MB total, 122.059 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.875, 18.349, 19.112)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.060899690259E+04 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #2 (complex-solv-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  122.059 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 4.276523673491E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (complex-ref-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  122.059 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.875, 18.349, 19.112)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.399234956777E+04 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #4 (complex-ref-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  122.059 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 4.610066575192E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #5 (dmso-solv-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  62.428 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 3.961107503213E+01 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #6 (dmso-solv-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  62.428 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 7.121048606059E+02 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #7 (dmso-ref-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  62.428 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 6.751571424823E+01 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #8 (dmso-ref-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  62.428 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 7.339101343121E+02 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #9 (1d7h-solv-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  121.736 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.875, 18.349, 19.112)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.058410584089E+04 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #10 (1d7h-solv-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  121.736 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 4.205385249581E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #11 (1d7h-ref-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  121.736 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.875, 18.349, 19.112)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.395961902233E+04 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #12 (1d7h-ref-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  121.736 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 4.538248433997E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end
+  Local net energy (PE 0) = -3.335429017008E+03 kJ/mol
+  Global net ELEC energy = -3.335429017008E+03 kJ/mol
+
+print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end
+  Local net energy (PE 0) = -2.180527370616E+01 kJ/mol
+  Global net ELEC energy = -2.180527370616E+01 kJ/mol
+
+print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end
+  Local net energy (PE 0) = -3.328631844166E+03 kJ/mol
+  Global net ELEC energy = -3.328631844166E+03 kJ/mol
+
+print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end
+  Local net energy (PE 0) = 1.500810086371E+01 kJ/mol
+  Global net ELEC energy = 1.500810086371E+01 kJ/mol
+----------------------------------------
+CLEANING UP AND SHUTTING DOWN...
+Destroying force arrays.
+No energy arrays to destroy.
+Destroying multigrid structures.
+Destroying finite element structures.
+Destroying 3 molecules
+Final memory usage:  0.001 MB total, 221.696 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/1d7h-dmso-smol.in

@@ -0,0 +1,287 @@
+##########################################################################
+# 1D7H/DMSO BINDING ENERGY
+##########################################################################
+
+read 
+  mol pqr 1d7h-dmso-complex.pqr 
+  mol pqr dmso-min.pqr 
+  mol pqr 1d7h-min.pqr
+end
+
+# COMPLEX -- SOLVATED STATE (FOCUSING)
+elec name complex-solv-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 1
+    mol 1
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name complex-solv-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 1
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# COMPLEX -- REFERENCE STATE (FOCUSING)
+elec name complex-ref-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 1
+    mol 1
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name complex-ref-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 1
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# DMSO -- SOLVATED STATE (FOCUSING)
+elec name dmso-solv-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name dmso-solv-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# DMSO -- REFERENCE STATE (FOCUSING)
+elec name dmso-ref-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name dmso-ref-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# 1D7H -- SOLVATED STATE (FOCUSING)
+elec name 1d7h-solv-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 3
+    mol 3
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name 1d7h-solv-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 3
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# 1D7H -- REFERENCE STATE (FOCUSING)
+elec name 1d7h-ref-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 3
+    mol 3
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name 1d7h-ref-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 3
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# COMPLEX SOLVATION ENERGY
+print elecEnergy complex-solv-fine - complex-ref-fine end
+
+# DMSO SOLVATION ENERGY
+print elecEnergy dmso-solv-fine - dmso-ref-fine end
+
+# 1D7H SOLVATION ENERGY
+print elecEnergy 1d7h-solv-fine - 1d7h-ref-fine end
+
+# CHANGE IN SOLVATION ENERGY UPON BINDING
+print elecEnergy complex-solv-fine - complex-ref-fine - dmso-solv-fine + dmso-ref-fine - 1d7h-solv-fine + 1d7h-ref-fine end
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/1d7h-dmso-smol.out

@@ -0,0 +1,449 @@
+
+
+----------------------------------------------------------------------
+    APBS -- Adaptive Poisson-Boltzmann Solver
+    Version APBS 3.4.1
+    
+    Nathan A. Baker (nathan.baker@pnnl.gov)
+    Pacific Northwest National Laboratory
+    
+    Additional contributing authors listed in the code documentation.
+    
+    Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
+    Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
+    Northwest Division for the U.S. Department of Energy.
+    
+    Portions Copyright (c) 2002-2010, Washington University in St. Louis.
+    Portions Copyright (c) 2002-2020, Nathan A. Baker.
+    Portions Copyright (c) 1999-2002, The Regents of the University of California.
+    Portions Copyright (c) 1995, Michael Holst.
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+    
+    * Redistributions of source code must retain the above copyright notice, this
+      list of conditions and the following disclaimer.
+    
+    * Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+    
+    * Neither the name of the developer nor the names of its contributors may be
+      used to endorse or promote products derived from this software without
+      specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+    ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+    ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+    (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+    LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+    ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+----------------------------------------------------------------------
+    APBS uses FETK (the Finite Element ToolKit) to solve the
+    Poisson-Boltzmann equation numerically.  FETK is a portable collection
+    of finite element modeling class libraries developed by the Michael Holst
+    research group and written in an object-oriented form of C.  FEtk is
+    designed to solve general coupled systems of nonlinear partial differential
+    equations using adaptive finite element methods, inexact Newton methods,
+    and algebraic multilevel methods.  More information about FEtk may be found
+    at <http://www.FEtk.ORG>.
+----------------------------------------------------------------------
+    APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
+    Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
+    which has been modified by Patrice Koehl
+    <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
+    memory usage when solving the Poisson-Boltzmann equation.
+----------------------------------------------------------------------
+    Please cite your use of APBS as:
+
+    Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
+    nanosystems: application to microtubules and the ribosome. Proc.
+    Natl. Acad. Sci. USA 98, 10037-10041 2001.
+    
+
+This executable compiled on Apr 29 2022 at 19:42:46
+
+Parsing input file 1d7h-dmso-smol.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from 1d7h-dmso-complex.pqr.
+  1673 atoms
+  Centered at (2.587e+01, 1.835e+01, 1.911e+01)
+  Net charge 9.91e-01 e
+Reading PQR-format atom data from dmso-min.pqr.
+  10 atoms
+  Centered at (1.775e+01, 1.777e+01, 2.049e+01)
+  Net charge 2.78e-17 e
+Reading PQR-format atom data from 1d7h-min.pqr.
+  1663 atoms
+  Centered at (2.587e+01, 1.835e+01, 1.911e+01)
+  Net charge 9.91e-01 e
+Preparing to run 12 PBE calculations.
+----------------------------------------
+CALCULATION #1 (complex-solv-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  122.059 MB total, 122.059 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.875, 18.349, 19.112)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.074948704824E+04 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #2 (complex-solv-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  122.059 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 4.289487256481E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (complex-ref-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  122.059 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.875, 18.349, 19.112)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.399234956777E+04 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #4 (complex-ref-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  122.059 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 4.610066575192E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #5 (dmso-solv-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  62.428 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 3.719709905887E+01 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #6 (dmso-solv-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  62.428 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 7.125747080979E+02 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #7 (dmso-ref-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  62.428 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 6.751571424823E+01 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #8 (dmso-ref-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  62.428 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 7.339101343121E+02 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #9 (1d7h-solv-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  121.736 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.875, 18.349, 19.112)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.071654753674E+04 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #10 (1d7h-solv-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  121.736 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 4.218178203716E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #11 (1d7h-ref-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  121.736 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.875, 18.349, 19.112)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.395961902233E+04 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #12 (1d7h-ref-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  121.736 MB total, 221.696 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.751, 17.770, 20.492)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 4.538248433997E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end
+  Local net energy (PE 0) = -3.205793187109E+03 kJ/mol
+  Global net ELEC energy = -3.205793187109E+03 kJ/mol
+
+print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end
+  Local net energy (PE 0) = -2.133542621421E+01 kJ/mol
+  Global net ELEC energy = -2.133542621421E+01 kJ/mol
+
+print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end
+  Local net energy (PE 0) = -3.200702302816E+03 kJ/mol
+  Global net ELEC energy = -3.200702302816E+03 kJ/mol
+
+print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end
+  Local net energy (PE 0) = 1.624454192073E+01 kJ/mol
+  Global net ELEC energy = 1.624454192073E+01 kJ/mol
+----------------------------------------
+CLEANING UP AND SHUTTING DOWN...
+Destroying force arrays.
+No energy arrays to destroy.
+Destroying multigrid structures.
+Destroying finite element structures.
+Destroying 3 molecules
+Final memory usage:  0.001 MB total, 221.696 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.inp

@@ -0,0 +1,343 @@
+!
+! Compute the binding energy of DMSO to
+! the active site of FKBP-12. This example
+! illustrates the use of focusing and the ability of UHBD to
+! handle mathematical operations specified by the user in
+! the input stream (see the assign statements below).
+!
+! Files: bindf.inp - this file
+!        1d7h-min.qcd - coords for FKBP with charges and radii
+!        dmso-min.qcd - coords for substrate (DMSO) with charges and radii
+!
+
+!
+! read in the coords., charges, and radii in CHARMM qcard
+! format
+!
+read mol 1 file "1d7h-min.qcd" qcard end ! FKBP
+read mol 2 file "dmso-min.qcd" qcard end ! DMSO
+
+!
+! Regular Runs:
+!               compute the potential on a coarse grid for
+!               molecule 1
+!
+
+elec calc mol 1
+ pdie   2.00                          ! internal dielectric=2
+ sdie  78.00                          ! solvent  dielectric=78
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   2                             ! boundary condition - each atom
+                                      ! is a Debye-Huckel sphere
+ efld    .00                          ! external electric field
+ grid   1.50                          ! grid spacing
+ dime   60  60  60                    ! grid dimension
+ center                               ! center the grid on the molecule
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phizero mol1 end           ! zero out the phisite accumulator
+print elec phisave mol1 end           ! compute and store phi at atoms on grid
+
+!  
+!               compute the potential on a fine grid
+!               molecule 1 using the coarse grid to set the
+!               boundary potentials for this grid.
+!
+
+elec calc mol 1
+ pdie   2.00                          ! internal dielectric=2
+ sdie  78.00                          ! solvent  dielectric=78
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   4                             ! focusing - use the coarse grid to
+                                      ! set the boundary potential of this
+                                      ! focused grid.
+ efld    .00                          ! external electric field
+ grid   0.225                         ! spacing for focused grid
+ dime   60  60  60                    ! grid dimension
+ mcenter 2
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phisave mol1 end
+print elec phiwrite mol1 end          ! write the phisite potentials to the output
+print elec phinrg mol1 end            ! compute and save to a user variable the
+                                      ! phi energy
+assign e1 = $phinrg end               ! assign the phi energy to a local variable 
+                                      ! for later use
+
+!
+! Reference Runs (i.e. self energy):
+!               coarse grid
+!               molecule 1
+!
+
+elec calc mol 1
+ pdie   2.00                          ! internal dielectric=2
+ sdie   2.00                          ! exterior dielectric=2. This is
+                                      ! the computation for the self
+                                      ! energy
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   2                             ! boundary condition - each atom
+                                      ! is a Debye-Huckel sphere
+ efld    .00                          ! external electric field
+ grid   1.50                          ! grid spacing
+ dime   60  60  60                    ! grid dimension
+ center                               ! center the grid on the molecule
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phizero mol1 end           ! zero out the phisite accumulator
+print elec phisave mol1 end           ! compute and store phi at atoms on grid
+
+!  
+!               fine grid
+!               molecule 1
+!
+
+elec calc mol 1
+ pdie   2.00                          ! internal dielectric=2
+ sdie   2.00                          ! exterior dielectric=2. This is
+                                      ! the copmputation for the self
+                                      ! energy
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   4                             ! focusing - use the coarse grid to
+                                      ! set the boundary potential of this
+                                      ! focused grid.
+ efld    .00                          ! external electric field
+ grid   0.225                         ! spacing for focused grid
+ dime   60  60  60                    ! grid dimension
+ mcenter 2
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phisave mol1 end
+print elec phinrg mol1 end  
+assign e2 = $phinrg end               ! save the phi "self" energy for mol1
+
+!
+! Regular Runs:
+!               coarse grid
+!               molecule 2
+!
+
+elec calc mol 2
+ pdie   2.00                          ! internal dielectric=2
+ sdie  78.00                          ! solvent  dielectric=78
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   2                             ! boundary condition - each atom
+                                      ! is a Debye-Huckel sphere
+ efld    .00                          ! external electric field
+ grid   1.50                          ! grid spacing
+ dime   60  60  60                    ! grid dimension
+ center                               ! center the grid on the molecule
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phizero mol2 end           ! zero out the phisite accumulator
+print elec phisave mol2 end           ! compute and store phi at atoms on grid
+
+!  
+!               fine grid
+!               molecule 2
+!
+
+elec calc mol 2
+ pdie   2.00                          ! internal dielectric=2
+ sdie  78.00                          ! solvent  dielectric=78
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   4                             ! focusing - use the coarse grid to
+                                      ! set the boundary potential of this
+                                      ! focused grid.
+ efld    .00                          ! external electric field
+ grid   0.225                         ! spacing for focused grid
+ dime   60  60  60                    ! grid dimension
+ mcenter 2
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phisave mol2 end
+print elec phinrg mol2 end  
+assign e3 = $phinrg end
+
+!
+! Reference Runs:
+!               coarse grid
+!               molecule 2
+!
+
+elec calc mol 2
+ pdie   2.00                          ! internal dielectric=2
+ sdie   2.00                          ! exterior dielectric=2. This is
+                                      ! the copmputation for the self
+                                      ! energy
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   2                             ! boundary condition - each atom
+                                      ! is a Debye-Huckel sphere
+ efld    .00                          ! external electric field
+ grid   1.50                          ! grid spacing
+ dime   60  60  60                    ! grid dimension
+ center                               ! center the grid on the molecule
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phizero mol2 end           ! zero out the phisite accumulator
+print elec phisave mol2 end           ! compute and store phi at atoms on grid
+
+!  
+!               fine grid
+!               molecule 2
+!
+
+elec calc mol 2
+ pdie   2.00                          ! internal dielectric=2
+ sdie   2.00                          ! exterior dielectric=2. This is
+                                      ! the copmputation for the self
+                                      ! energy
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   4                             ! focusing - use the coarse grid to
+                                      ! set the boundary potential of this
+                                      ! focused grid.
+ efld    .00                          ! external electric field
+ grid   0.225                         ! spacing for focused grid
+ dime   60  60  60                    ! grid dimension
+ mcenter 2
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phisave mol2 end
+print elec phinrg mol2 end  
+assign e4 = $phinrg end
+
+!
+! Regular Runs:
+!               coarse grid
+!               molecule complex
+!
+
+elec calc all 
+ pdie   2.00                          ! internal dielectric=2
+ sdie  78.00                          ! solvent  dielectric=78
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   2                             ! boundary condition - each atom
+                                      ! is a Debye-Huckel sphere
+ efld    .00                          ! external electric field
+ grid   1.50                          ! grid spacing
+ dime   60  60  60                    ! grid dimension
+ center                               ! center the grid on the molecule
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phizero all end            ! zero out the phisite accumulator
+print elec phisave all end            ! compute and store phi at atoms on grid
+
+!  
+!               fine grid
+!               molecule complex
+!
+
+elec calc all 
+ pdie   2.00                          ! internal dielectric=2
+ sdie  78.00                          ! solvent  dielectric=78
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   4                             ! focusing - use the coarse grid to
+                                      ! set the boundary potential of this
+                                      ! focused grid.
+ efld    .00                          ! external electric field
+ grid   0.225                         ! spacing for focused grid
+ dime   60  60  60                    ! grid dimension
+ mcenter 2
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phisave all end
+print elec phinrg all end  
+assign e5 = $phinrg end
+
+!
+! Reference Runs:
+!               coarse grid
+!               molecule complex
+!
+
+elec calc  all
+ pdie   2.00                          ! internal dielectric=2
+ sdie   2.00                          ! exterior dielectric=2. This is
+                                      ! the copmputation for the self
+                                      ! energy
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   2                             ! boundary condition - each atom
+                                      ! is a Debye-Huckel sphere
+ efld    .00                          ! external electric field
+ grid   1.50                          ! grid spacing
+ dime   60  60  60                    ! grid dimension
+ center                               ! center the grid on the molecule
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phizero all end            ! zero out the phisite accumulator
+print elec phisave all end            ! compute and store phi at atoms on grid
+
+!  
+!               fine grid
+!               molecule complex
+!
+
+elec calc all
+ pdie   2.00                          ! internal dielectric=2
+ sdie   2.00                          ! exterior dielectric=2. This is
+                                      ! the copmputation for the self
+                                      ! energy
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   4                             ! focusing - use the coarse grid to
+                                      ! set the boundary potential of this
+                                      ! focused grid.
+ efld    .00                          ! external electric field
+ grid   0.225                         ! spacing for focused grid
+ dime   60  60  60                    ! grid dimension
+ mcenter 2
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phisave all end
+print elec phinrg all end  
+assign e6 = $phinrg end
+
+print mcou 1 2 end                    ! print the electrostatic interaction
+                                      ! between mol1 and mol2
+assign ecoul12 = $mcou end
+
+!
+! Now compute the solvation energies of mol1, mol2, the mol1-mol2
+! complex and the coulombic interaction metween mol1 and mol2. The
+! binding energy is then: esolv12 - (esolv1 + esolv2) + ecoul12.
+
+assign
+  esolv1 = $e1 $e2 -
+end
+assign
+  esolv2 = $e3 $e4 -
+end
+assign
+  esolv12 = $e5 $e6 -
+end
+assign
+  ebind = $esolv12 
+          $esolv1 -
+          $esolv2 -
+          $ecoul12 +
+end
+
+stop

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/1d7h-dmso/UHBD/dmso-min.qcd

@@ -0,0 +1,12 @@
+ATOM   108 DMS  S      18.698  17.176  20.771   0.194   1.996
+ATOM   108 DMS  O      18.156  16.050  21.663  -0.510   1.658
+ATOM   108 DMS  C1     17.782  17.180  19.226  -0.082   1.904
+ATOM   108 DMS  C2     18.196  18.764  21.428  -0.082   1.904
+ATOM   108 DMS  H5     18.469  19.489  20.794   0.080   1.484
+ATOM   108 DMS  H6     18.636  18.913  22.313   0.080   1.484
+ATOM   108 DMS  H7     17.203  18.779  21.543   0.080   1.484
+ATOM   108 DMS  H8     16.804  17.251  19.418   0.080   1.484
+ATOM   108 DMS  H9     17.964  16.332  18.728   0.080   1.484
+ATOM   108 DMS  H10    18.069  17.960  18.670   0.080   1.484
+TER
+END

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/1d7h-dmso/UHBD/pqr2qcd

@@ -0,0 +1,2 @@
+#! /bin/sh
+cat $1 | sed -f amber2charmm_sed.scr | awk '{if ($1=="ATOM" ) {printf ("%-6s%4d %-4s %-4s %8.3f%8.3f%8.3f%8.3f%8.3f\n",$1,$5,$4,$3,$6,$7,$8,$9,$10)} else {print}}' > $2 

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/1d7i-dss-mol.in

@@ -0,0 +1,287 @@
+##########################################################################
+# 1D7I/DSS BINDING ENERGY
+##########################################################################
+
+read 
+  mol pqr 1d7i-dss-complex.pqr 
+  mol pqr dss-min.pqr 
+  mol pqr 1d7i-min.pqr
+end
+
+# COMPLEX -- SOLVATED STATE (FOCUSING)
+elec name complex-solv-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 1
+    mol 1
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name complex-solv-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 1
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# COMPLEX -- REFERENCE STATE (FOCUSING)
+elec name complex-ref-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 1
+    mol 1
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name complex-ref-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 1
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# DSS -- SOLVATED STATE (FOCUSING)
+elec name dss-solv-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name dss-solv-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# DSS -- REFERENCE STATE (FOCUSING)
+elec name dss-ref-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name dss-ref-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# 1D7I -- SOLVATED STATE (FOCUSING)
+elec name 1d7i-solv-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 3
+    mol 3
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name 1d7i-solv-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 3
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# 1D7I -- REFERENCE STATE (FOCUSING)
+elec name 1d7i-ref-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 3
+    mol 3
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name 1d7i-ref-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 3
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm mol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# COMPLEX SOLVATION ENERGY
+print elecEnergy complex-solv-fine - complex-ref-fine end
+
+# DSS SOLVATION ENERGY
+print elecEnergy dss-solv-fine - dss-ref-fine end
+
+# 1D7H SOLVATION ENERGY
+print elecEnergy 1d7i-solv-fine - 1d7i-ref-fine end
+
+# CHANGE IN SOLVATION ENERGY UPON BINDING
+print elecEnergy complex-solv-fine - complex-ref-fine - dss-solv-fine + dss-ref-fine - 1d7i-solv-fine + 1d7i-ref-fine end
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/1d7i-dss-mol.out

@@ -0,0 +1,449 @@
+
+
+----------------------------------------------------------------------
+    APBS -- Adaptive Poisson-Boltzmann Solver
+    Version APBS 3.4.1
+    
+    Nathan A. Baker (nathan.baker@pnnl.gov)
+    Pacific Northwest National Laboratory
+    
+    Additional contributing authors listed in the code documentation.
+    
+    Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
+    Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
+    Northwest Division for the U.S. Department of Energy.
+    
+    Portions Copyright (c) 2002-2010, Washington University in St. Louis.
+    Portions Copyright (c) 2002-2020, Nathan A. Baker.
+    Portions Copyright (c) 1999-2002, The Regents of the University of California.
+    Portions Copyright (c) 1995, Michael Holst.
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+    
+    * Redistributions of source code must retain the above copyright notice, this
+      list of conditions and the following disclaimer.
+    
+    * Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+    
+    * Neither the name of the developer nor the names of its contributors may be
+      used to endorse or promote products derived from this software without
+      specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+    ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+    ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+    (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+    LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+    ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+----------------------------------------------------------------------
+    APBS uses FETK (the Finite Element ToolKit) to solve the
+    Poisson-Boltzmann equation numerically.  FETK is a portable collection
+    of finite element modeling class libraries developed by the Michael Holst
+    research group and written in an object-oriented form of C.  FEtk is
+    designed to solve general coupled systems of nonlinear partial differential
+    equations using adaptive finite element methods, inexact Newton methods,
+    and algebraic multilevel methods.  More information about FEtk may be found
+    at <http://www.FEtk.ORG>.
+----------------------------------------------------------------------
+    APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
+    Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
+    which has been modified by Patrice Koehl
+    <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
+    memory usage when solving the Poisson-Boltzmann equation.
+----------------------------------------------------------------------
+    Please cite your use of APBS as:
+
+    Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
+    nanosystems: application to microtubules and the ribosome. Proc.
+    Natl. Acad. Sci. USA 98, 10037-10041 2001.
+    
+
+This executable compiled on Apr 29 2022 at 19:42:46
+
+Parsing input file 1d7i-dss-mol.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from 1d7i-dss-complex.pqr.
+  1677 atoms
+  Centered at (2.526e+01, 1.899e+01, 1.912e+01)
+  Net charge 9.91e-01 e
+Reading PQR-format atom data from dss-min.pqr.
+  14 atoms
+  Centered at (1.734e+01, 1.921e+01, 2.050e+01)
+  Net charge -8.33e-17 e
+Reading PQR-format atom data from 1d7i-min.pqr.
+  1663 atoms
+  Centered at (2.526e+01, 1.899e+01, 1.912e+01)
+  Net charge 9.91e-01 e
+Preparing to run 12 PBE calculations.
+----------------------------------------
+CALCULATION #1 (complex-solv-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  122.425 MB total, 122.425 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.264, 18.988, 19.122)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 9.160578033846E+03 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #2 (complex-solv-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  122.425 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 3.955701871716E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (complex-ref-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  122.425 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.264, 18.988, 19.122)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.264965939588E+04 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #4 (complex-ref-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  122.425 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 4.301801664829E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #5 (dss-solv-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  62.528 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 9.431133325426E+01 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #6 (dss-solv-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  62.528 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.677348113184E+03 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #7 (dss-ref-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  62.528 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.171079106781E+02 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #8 (dss-ref-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  62.528 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.697869784185E+03 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #9 (1d7i-solv-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  121.977 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.264, 18.988, 19.122)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 9.040108332204E+03 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #10 (1d7i-solv-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  121.977 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 3.787747796627E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #11 (1d7i-ref-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  121.977 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.264, 18.988, 19.122)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.252495566243E+04 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #12 (1d7i-ref-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  121.977 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 4.133237922574E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end
+  Local net energy (PE 0) = -3.460997931137E+03 kJ/mol
+  Global net ELEC energy = -3.460997931137E+03 kJ/mol
+
+print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end
+  Local net energy (PE 0) = -2.052167100108E+01 kJ/mol
+  Global net ELEC energy = -2.052167100108E+01 kJ/mol
+
+print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end
+  Local net energy (PE 0) = -3.454901259473E+03 kJ/mol
+  Global net ELEC energy = -3.454901259473E+03 kJ/mol
+
+print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end
+  Local net energy (PE 0) = 1.442499933668E+01 kJ/mol
+  Global net ELEC energy = 1.442499933668E+01 kJ/mol
+----------------------------------------
+CLEANING UP AND SHUTTING DOWN...
+Destroying force arrays.
+No energy arrays to destroy.
+Destroying multigrid structures.
+Destroying finite element structures.
+Destroying 3 molecules
+Final memory usage:  0.001 MB total, 222.305 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/1d7i-dss-smol.in

@@ -0,0 +1,287 @@
+##########################################################################
+# 1D7I/DSS BINDING ENERGY
+##########################################################################
+
+read 
+  mol pqr 1d7i-dss-complex.pqr 
+  mol pqr dss-min.pqr 
+  mol pqr 1d7i-min.pqr
+end
+
+# COMPLEX -- SOLVATED STATE (FOCUSING)
+elec name complex-solv-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 1
+    mol 1
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name complex-solv-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 1
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# COMPLEX -- REFERENCE STATE (FOCUSING)
+elec name complex-ref-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 1
+    mol 1
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name complex-ref-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 1
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# DSS -- SOLVATED STATE (FOCUSING)
+elec name dss-solv-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name dss-solv-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# DSS -- REFERENCE STATE (FOCUSING)
+elec name dss-ref-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name dss-ref-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 2
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# 1D7I -- SOLVATED STATE (FOCUSING)
+elec name 1d7i-solv-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 3
+    mol 3
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name 1d7i-solv-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 3
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie 78.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# 1D7I -- REFERENCE STATE (FOCUSING)
+elec name 1d7i-ref-coarse
+    mg-manual
+    dime 65 65 65
+    grid 1.5 1.5 1.5
+    gcent mol 3
+    mol 3
+    lpbe
+    bcfl mdh
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+elec name 1d7i-ref-fine
+    mg-manual
+    dime 65 65 65
+    grid 0.225 0.225 0.225
+    gcent mol 2
+    mol 3
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.010 radius 2.0
+    ion charge -1 conc 0.010 radius 2.0
+    pdie  2.0
+    sdie  2.0
+    srfm smol
+    chgm spl0
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 300
+    calcenergy total
+    calcforce no
+end
+
+# COMPLEX SOLVATION ENERGY
+print elecEnergy complex-solv-fine - complex-ref-fine end
+
+# DSS SOLVATION ENERGY
+print elecEnergy dss-solv-fine - dss-ref-fine end
+
+# 1D7H SOLVATION ENERGY
+print elecEnergy 1d7i-solv-fine - 1d7i-ref-fine end
+
+# CHANGE IN SOLVATION ENERGY UPON BINDING
+print elecEnergy complex-solv-fine - complex-ref-fine - dss-solv-fine + dss-ref-fine - 1d7i-solv-fine + 1d7i-ref-fine end
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/1d7i-dss-smol.out

@@ -0,0 +1,449 @@
+
+
+----------------------------------------------------------------------
+    APBS -- Adaptive Poisson-Boltzmann Solver
+    Version APBS 3.4.1
+    
+    Nathan A. Baker (nathan.baker@pnnl.gov)
+    Pacific Northwest National Laboratory
+    
+    Additional contributing authors listed in the code documentation.
+    
+    Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
+    Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
+    Northwest Division for the U.S. Department of Energy.
+    
+    Portions Copyright (c) 2002-2010, Washington University in St. Louis.
+    Portions Copyright (c) 2002-2020, Nathan A. Baker.
+    Portions Copyright (c) 1999-2002, The Regents of the University of California.
+    Portions Copyright (c) 1995, Michael Holst.
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+    
+    * Redistributions of source code must retain the above copyright notice, this
+      list of conditions and the following disclaimer.
+    
+    * Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+    
+    * Neither the name of the developer nor the names of its contributors may be
+      used to endorse or promote products derived from this software without
+      specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+    ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+    ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+    (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+    LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+    ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+----------------------------------------------------------------------
+    APBS uses FETK (the Finite Element ToolKit) to solve the
+    Poisson-Boltzmann equation numerically.  FETK is a portable collection
+    of finite element modeling class libraries developed by the Michael Holst
+    research group and written in an object-oriented form of C.  FEtk is
+    designed to solve general coupled systems of nonlinear partial differential
+    equations using adaptive finite element methods, inexact Newton methods,
+    and algebraic multilevel methods.  More information about FEtk may be found
+    at <http://www.FEtk.ORG>.
+----------------------------------------------------------------------
+    APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
+    Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
+    which has been modified by Patrice Koehl
+    <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
+    memory usage when solving the Poisson-Boltzmann equation.
+----------------------------------------------------------------------
+    Please cite your use of APBS as:
+
+    Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
+    nanosystems: application to microtubules and the ribosome. Proc.
+    Natl. Acad. Sci. USA 98, 10037-10041 2001.
+    
+
+This executable compiled on Apr 29 2022 at 19:42:46
+
+Parsing input file 1d7i-dss-smol.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from 1d7i-dss-complex.pqr.
+  1677 atoms
+  Centered at (2.526e+01, 1.899e+01, 1.912e+01)
+  Net charge 9.91e-01 e
+Reading PQR-format atom data from dss-min.pqr.
+  14 atoms
+  Centered at (1.734e+01, 1.921e+01, 2.050e+01)
+  Net charge -8.33e-17 e
+Reading PQR-format atom data from 1d7i-min.pqr.
+  1663 atoms
+  Centered at (2.526e+01, 1.899e+01, 1.912e+01)
+  Net charge 9.91e-01 e
+Preparing to run 12 PBE calculations.
+----------------------------------------
+CALCULATION #1 (complex-solv-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  122.425 MB total, 122.425 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.264, 18.988, 19.122)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 9.634884642408E+03 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #2 (complex-solv-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  122.425 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 4.003177540425E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (complex-ref-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  122.425 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.264, 18.988, 19.122)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.264965939588E+04 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #4 (complex-ref-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  122.425 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 4.301801664829E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #5 (dss-solv-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  62.528 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 7.942232645345E+01 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #6 (dss-solv-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  62.528 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.677798535473E+03 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #7 (dss-ref-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  62.528 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.171079106781E+02 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #8 (dss-ref-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  62.528 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.697869784185E+03 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #9 (1d7i-solv-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  121.977 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.264, 18.988, 19.122)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 9.507068451372E+03 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #10 (1d7i-solv-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  30.4176 A
+  Current memory usage:  121.977 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 3.835075772299E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #11 (1d7i-ref-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  121.977 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 1.500 x 1.500 x 1.500
+  Grid lengths: 96.000 x 96.000 x 96.000
+  Grid center: (25.264, 18.988, 19.122)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.252495566243E+04 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #12 (1d7i-ref-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  4.87072 A
+  Current memory usage:  121.977 MB total, 222.305 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.225 x 0.225 x 0.225
+  Grid lengths: 14.400 x 14.400 x 14.400
+  Grid center: (17.340, 19.211, 20.503)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.010 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.010 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.010 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 2.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  300.000 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 4.133237922574E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end
+  Local net energy (PE 0) = -2.986241244040E+03 kJ/mol
+  Global net ELEC energy = -2.986241244040E+03 kJ/mol
+
+print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end
+  Local net energy (PE 0) = -2.007124871262E+01 kJ/mol
+  Global net ELEC energy = -2.007124871262E+01 kJ/mol
+
+print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end
+  Local net energy (PE 0) = -2.981621502756E+03 kJ/mol
+  Global net ELEC energy = -2.981621502756E+03 kJ/mol
+
+print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end
+  Local net energy (PE 0) = 1.545150742844E+01 kJ/mol
+  Global net ELEC energy = 1.545150742844E+01 kJ/mol
+----------------------------------------
+CLEANING UP AND SHUTTING DOWN...
+Destroying force arrays.
+No energy arrays to destroy.
+Destroying multigrid structures.
+Destroying finite element structures.
+Destroying 3 molecules
+Final memory usage:  0.001 MB total, 222.305 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.inp

@@ -0,0 +1,343 @@
+!
+! Compute the binding energy of DSS to
+! the active site of FKBP-12. This example
+! illustrates the use of focusing and the ability of UHBD to
+! handle mathematical operations specified by the user in
+! the input stream (see the assign statements below).
+!
+! Files: bindf.inp - this file
+!        1d7i-min.qcd - coords for FKBP with charges and radii
+!        dss-min.qcd - coords for substrate (DSS) with charges and radii
+!
+
+!
+! read in the coords., charges, and radii in CHARMM qcard
+! format
+!
+read mol 1 file "1d7i-min.qcd" qcard end ! FKBP
+read mol 2 file "dss-min.qcd" qcard end  ! DSS
+
+!
+! Regular Runs:
+!               compute the potential on a coarse grid for
+!               molecule 1
+!
+
+elec calc mol 1
+ pdie   2.00                          ! internal dielectric=2
+ sdie  78.00                          ! solvent  dielectric=78
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   2                             ! boundary condition - each atom
+                                      ! is a Debye-Huckel sphere
+ efld    .00                          ! external electric field
+ grid   1.50                          ! grid spacing
+ dime   60  60  60                    ! grid dimension
+ center                               ! center the grid on the molecule
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phizero mol1 end           ! zero out the phisite accumulator
+print elec phisave mol1 end           ! compute and store phi at atoms on grid
+
+!  
+!               compute the potential on a fine grid
+!               molecule 1 using the coarse grid to set the
+!               boundary potentials for this grid.
+!
+
+elec calc mol 1
+ pdie   2.00                          ! internal dielectric=2
+ sdie  78.00                          ! solvent  dielectric=78
+ temp 300.00                          ! temperature in K
+ ions    .00                          ! ionic strength
+ bcfl   4                             ! focusing - use the coarse grid to
+                                      ! set the boundary potential of this
+                                      ! focused grid.
+ efld    .00                          ! external electric field
+ grid   0.225                         ! spacing for focused grid
+ dime   60  60  60                    ! grid dimension
+ mcenter 2
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phisave mol1 end
+print elec phiwrite mol1 end          ! write the phisite potentials to the output
+print elec phinrg mol1 end            ! compute and save to a user variable the
+                                      ! phi energy
+assign e1 = $phinrg end               ! assign the phi energy to a local variable 
+                                      ! for later use
+
+!
+! Reference Runs (i.e. self energy):
+!               coarse grid
+!               molecule 1
+!
+
+elec calc mol 1
+ pdie   2.00                          ! internal dielectric=2
+ sdie   2.00                          ! exterior dielectric=2. This is
+                                      ! the computation for the self
+                                      ! energy
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   2                             ! boundary condition - each atom
+                                      ! is a Debye-Huckel sphere
+ efld    .00                          ! external electric field
+ grid   1.50                          ! grid spacing
+ dime   60  60  60                    ! grid dimension
+ center                               ! center the grid on the molecule
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phizero mol1 end           ! zero out the phisite accumulator
+print elec phisave mol1 end           ! compute and store phi at atoms on grid
+
+!  
+!               fine grid
+!               molecule 1
+!
+
+elec calc mol 1
+ pdie   2.00                          ! internal dielectric=2
+ sdie   2.00                          ! exterior dielectric=2. This is
+                                      ! the copmputation for the self
+                                      ! energy
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   4                             ! focusing - use the coarse grid to
+                                      ! set the boundary potential of this
+                                      ! focused grid.
+ efld    .00                          ! external electric field
+ grid   0.225                         ! spacing for focused grid
+ dime   60  60  60                    ! grid dimension
+ mcenter 2
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phisave mol1 end
+print elec phinrg mol1 end  
+assign e2 = $phinrg end               ! save the phi "self" energy for mol1
+
+!
+! Regular Runs:
+!               coarse grid
+!               molecule 2
+!
+
+elec calc mol 2
+ pdie   2.00                          ! internal dielectric=2
+ sdie  78.00                          ! solvent  dielectric=78
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   2                             ! boundary condition - each atom
+                                      ! is a Debye-Huckel sphere
+ efld    .00                          ! external electric field
+ grid   1.50                          ! grid spacing
+ dime   60  60  60                    ! grid dimension
+ center                               ! center the grid on the molecule
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phizero mol2 end           ! zero out the phisite accumulator
+print elec phisave mol2 end           ! compute and store phi at atoms on grid
+
+!  
+!               fine grid
+!               molecule 2
+!
+
+elec calc mol 2
+ pdie   2.00                          ! internal dielectric=2
+ sdie  78.00                          ! solvent  dielectric=78
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   4                             ! focusing - use the coarse grid to
+                                      ! set the boundary potential of this
+                                      ! focused grid.
+ efld    .00                          ! external electric field
+ grid   0.225                         ! spacing for focused grid
+ dime   60  60  60                    ! grid dimension
+ mcenter 2
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phisave mol2 end
+print elec phinrg mol2 end  
+assign e3 = $phinrg end
+
+!
+! Reference Runs:
+!               coarse grid
+!               molecule 2
+!
+
+elec calc mol 2
+ pdie   2.00                          ! internal dielectric=2
+ sdie   2.00                          ! exterior dielectric=2. This is
+                                      ! the copmputation for the self
+                                      ! energy
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   2                             ! boundary condition - each atom
+                                      ! is a Debye-Huckel sphere
+ efld    .00                          ! external electric field
+ grid   1.50                          ! grid spacing
+ dime   60  60  60                    ! grid dimension
+ center                               ! center the grid on the molecule
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phizero mol2 end           ! zero out the phisite accumulator
+print elec phisave mol2 end           ! compute and store phi at atoms on grid
+
+!  
+!               fine grid
+!               molecule 2
+!
+
+elec calc mol 2
+ pdie   2.00                          ! internal dielectric=2
+ sdie   2.00                          ! exterior dielectric=2. This is
+                                      ! the copmputation for the self
+                                      ! energy
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   4                             ! focusing - use the coarse grid to
+                                      ! set the boundary potential of this
+                                      ! focused grid.
+ efld    .00                          ! external electric field
+ grid   0.225                         ! spacing for focused grid
+ dime   60  60  60                    ! grid dimension
+ mcenter 2
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phisave mol2 end
+print elec phinrg mol2 end  
+assign e4 = $phinrg end
+
+!
+! Regular Runs:
+!               coarse grid
+!               molecule complex
+!
+
+elec calc all 
+ pdie   2.00                          ! internal dielectric=2
+ sdie  78.00                          ! solvent  dielectric=78
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   2                             ! boundary condition - each atom
+                                      ! is a Debye-Huckel sphere
+ efld    .00                          ! external electric field
+ grid   1.50                          ! grid spacing
+ dime   60  60  60                    ! grid dimension
+ center                               ! center the grid on the molecule
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phizero all end            ! zero out the phisite accumulator
+print elec phisave all end            ! compute and store phi at atoms on grid
+
+!  
+!               fine grid
+!               molecule complex
+!
+
+elec calc all 
+ pdie   2.00                          ! internal dielectric=2
+ sdie  78.00                          ! solvent  dielectric=78
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   4                             ! focusing - use the coarse grid to
+                                      ! set the boundary potential of this
+                                      ! focused grid.
+ efld    .00                          ! external electric field
+ grid   0.225                         ! spacing for focused grid
+ dime   60  60  60                    ! grid dimension
+ mcenter 2
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phisave all end
+print elec phinrg all end  
+assign e5 = $phinrg end
+
+!
+! Reference Runs:
+!               coarse grid
+!               molecule complex
+!
+
+elec calc  all
+ pdie   2.00                          ! internal dielectric=2
+ sdie   2.00                          ! exterior dielectric=2. This is
+                                      ! the copmputation for the self
+                                      ! energy
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   2                             ! boundary condition - each atom
+                                      ! is a Debye-Huckel sphere
+ efld    .00                          ! external electric field
+ grid   1.50                          ! grid spacing
+ dime   60  60  60                    ! grid dimension
+ center                               ! center the grid on the molecule
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phizero all end            ! zero out the phisite accumulator
+print elec phisave all end            ! compute and store phi at atoms on grid
+
+!  
+!               fine grid
+!               molecule complex
+!
+
+elec calc all
+ pdie   2.00                          ! internal dielectric=2
+ sdie   2.00                          ! exterior dielectric=2. This is
+                                      ! the copmputation for the self
+                                      ! energy
+ temp 300.00                          ! temperature in K
+ ions   0.10                          ! ionic strength
+ bcfl   4                             ! focusing - use the coarse grid to
+                                      ! set the boundary potential of this
+                                      ! focused grid.
+ efld    .00                          ! external electric field
+ grid   0.225                         ! spacing for focused grid
+ dime   60  60  60                    ! grid dimension
+ mcenter 2
+ maxit 200                            ! maximum # of iteration for FDPBE
+end
+
+print elec phisave all end
+print elec phinrg all end  
+assign e6 = $phinrg end
+
+print mcou 1 2 end                    ! print the electrostatic interaction
+                                      ! between mol1 and mol2
+assign ecoul12 = $mcou end
+
+!
+! Now compute the solvation energies of mol1, mol2, the mol1-mol2
+! complex and the coulombic interaction metween mol1 and mol2. The
+! binding energy is then: esolv12 - (esolv1 + esolv2) + ecoul12.
+
+assign
+  esolv1 = $e1 $e2 -
+end
+assign
+  esolv2 = $e3 $e4 -
+end
+assign
+  esolv12 = $e5 $e6 -
+end
+assign
+  ebind = $esolv12 
+          $esolv1 -
+          $esolv2 -
+          $ecoul12 +
+end
+
+stop

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/1d7i-dss/UHBD/dss-min.qcd

@@ -0,0 +1,14 @@
+ATOM   108 DSS  S      18.252  17.192  20.920   0.349   1.996
+ATOM   108 DSS  O      17.730  16.166  21.890  -0.541   1.658
+ATOM   108 DSS  C1     17.418  16.962  19.356   0.004   1.904
+ATOM   108 DSS  C2     17.541  18.705  21.324  -0.359   1.904
+ATOM   108 DSS  S3     18.085  20.050  20.263  -0.190   1.996
+ATOM   108 DSS  C4     17.631  21.458  21.373  -0.168   1.904
+ATOM   108 DSS  H7     16.429  16.942  19.505   0.052   1.484
+ATOM   108 DSS  H8     17.711  16.099  18.946   0.052   1.484
+ATOM   108 DSS  H9     17.646  17.717  18.742   0.052   1.484
+ATOM   108 DSS  H10    17.781  18.947  22.264   0.220   1.484
+ATOM   108 DSS  H11    16.546  18.639  21.242   0.220   1.484
+ATOM   108 DSS  H12    16.647  21.438  21.553   0.103   1.484
+ATOM   108 DSS  H13    17.870  22.323  20.931   0.103   1.484
+ATOM   108 DSS  H14    18.129  21.377  22.236   0.103   1.484

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/README.md

@@ -0,0 +1,108 @@
+README for FKBP APBS examples
+=============================
+
+The example input files in this directory simulate the binding of various (small) ligands to FKBP. Analogous to HCA binding case (except it works).
+
+In order to calculate solvation energy upon binding you will need to take the results from these input files and subtract from them the results obtained from the `coulomb` utility found at `apbs/tools/manip/coulomb`. The values returned from this utility are:
+
+-   1d7h-dmso: -15.0930 kJ/mol (analytical value -15.103 kJ/mol)
+-   1d7i-dss: -11.9670 kJ/mol (analytical value -11.975 kJ/mol)
+
+This example was contributed by Jung-Hsin Lin.
+
+Input File|Description|APBS Version|Results (kJ/mol)|UHBD (kJ/mol)
+---|---|---|---|---
+[1d7h-dmso/apbs-mol.in](1d7h-dmso/apbs-mol.in)|1d7h-dmso, 2-level focusing to 0.225 A, VdW surface, srfm mol|**3.0**|**15.0081**|**19.097**
+|||1.5|15.0081
+|||1.4.2|15.0081
+|||1.4.1|15.0081
+|||1.4|15.0081<sup>[4](#4)</sup>
+|||1.3|15.0077
+|||1.2.1|15.0077<sup>[3](#3)</sup>
+|||1.2|15.0087<sup>[2](#2)</sup>
+|||1.1.0|15.0089
+|||1.0.0|15.0089
+|||0.5.1|15.0089
+|||0.5.0|15.0089
+|||0.4.0|15.0089
+[1d7h-dmso/apbs-smol.in](1d7h-dmso/apbs-smol.in)|1d7h-dmso, 2-level focusing to 0.225 A, VdW surface, srfm smol|**3.0**|**16.2445**|**19.097**
+|||1.5|16.2445
+|||1.4.2|16.2445
+|||1.4.1|16.2445
+|||1.4|16.2445<sup>[4](#4)</sup>
+|||1.3|16.2446
+|||1.2.1|16.2446<sup>[3](#3)</sup>
+|||1.2|16.2456<sup>[2](#2)</sup>
+|||1.1.0|16.2458
+|||1.0.0|16.2458
+|||0.5.1|16.2458
+|||0.5.0|16.2458
+|||0.4.0|16.2458<sup>[1](#1)</sup>
+|||0.3.2|15.0089
+|||0.3.1|15.0089
+|||0.3.0|15.0089
+|||0.2.6|15.0089
+|||0.2.5|15.0089
+|||0.2.4|15.0089
+|||0.2.3|15.0097
+|||0.2.2|14.5886
+|||0.2.1|14.589
+|||0.2.0|14.589
+|||0.1.8|14.591
+[1d7i-dss/apbs-mol.in](1d7i-dss/apbs-mol.in)|1d7i-dss, 2-level focusing to 0.225 A, VdW surface, srfm mol|**3.0**|**14.4250**|**16.231**
+|||1.5|14.4250
+|||1.4.2|14.4250
+|||1.4.1|14.4250
+|||1.4|14.4250
+|||1.3|14.4250
+|||1.2.1|14.4250<sup>[3](#3)</sup>
+|||1.2|14.4253<sup>[2](#2)</sup>
+|||1.1.0|14.4254
+|||1.0.0|14.4254
+|||0.5.1|14.4254
+|||0.5.0|14.4254
+|||0.4.0|14.4254
+[1d7i-dss/apbs-smol.in](1d7i-dss/apbs-smol.in)|1d7i-dss, 2-level focusing to 0.225 A, VdW surface, srfm smol|**3.0**|**15.4515**|**16.231**
+|||1.5|15.4515
+|||1.4.2|15.4515
+|||1.4.1|15.4515
+|||1.4|15.4515
+|||1.3|15.4515
+|||1.2.1|15.4515<sup>[3](#3)</sup>
+|||1.2|15.4517
+|||1.1.0|15.4517
+|||1.0.0|15.4517
+|||0.5.1|15.4517
+|||0.5.0|15.4517
+|||0.4.0|15.4517<sup>[1](#1)</sup>
+|||0.3.2|14.4254
+|||0.3.1|14.4254
+|||0.3.0|14.4254
+|||0.2.6|14.4254
+|||0.2.5|14.4254
+|||0.2.4|14.4254
+|||0.2.3|14.4254
+|||0.2.2|14.3865
+|||0.2.1|14.387
+|||0.2.0|14.387
+|||0.1.8|15.210
+
+<a name=1></a><sup>1</sup> The discrepancy in values between versions 0.4.0 and 0.3.2 is most likely due to three factors:
+
+-   A bug fix in Vacc\_molAcc which removed spurious regions of high internal dielectric values
+-   A switch in the algorithm used to compute the dielectric smoothing for srfm smol
+-   The addition of the Vacc sphere density (sdens keyword) as a variable and a change in the default sdens value from 3.0 to 10.0
+
+<a name=2></a><sup>2</sup> APBS 1.2 has switched the multigrid smoothing algorithm from standard Gauss-Seidel to Gauss-Seidel red/black in order to facilitate parallelization. This switch has caused small differences in individual calculation energies which, when combined to the final answer, create larger errors (up to 0.04%). These errors can be reduced by resetting the APBS error tolerance to 1e-9 or smaller values. For a more detailed explanation, please see the APBS FAQ, [here](http://www.poissonboltzmann.org/docs/apbs-faq/#sources error calculation).
+
+<a name=3></a><sup>3</sup> The discrepancy in values between versions 1.2 and 1.2.1 is most likely due to the following factor(s):
+
+-   Fixed a bug in Vpmg\_fillcoCoefMolIon which causes npbe based calculations to return very large energies
+
+<a name=4></a><sup>4</sup> The discrepancy in values between versions 1.3 and 1.4 is most likely due to the following factor(s):
+
+-   Translation of contrib/pmgZ library from FORTRAN to C
+-   Differences in numerical implementations between FORTRAN and C compilers result in small round-off discrepencies
+-   Small margins due to these round-off discrepencies acumulate in the computations
+
+Please see the ChangeLog or the [APBS website](http://www.poissonboltzmann.org/) for more information.

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/dmso-min.pqr

@@ -0,0 +1,12 @@
+ATOM   1664  S   DMS   108      18.698  17.176  20.771   0.194   1.996
+ATOM   1665  O   DMS   108      18.156  16.050  21.663  -0.510   1.658
+ATOM   1666  C1  DMS   108      17.782  17.180  19.226  -0.082   1.904
+ATOM   1667  C2  DMS   108      18.196  18.764  21.428  -0.082   1.904
+ATOM   1668  H5  DMS   108      18.469  19.489  20.794   0.080   1.484
+ATOM   1669  H6  DMS   108      18.636  18.913  22.313   0.080   1.484
+ATOM   1670  H7  DMS   108      17.203  18.779  21.543   0.080   1.484
+ATOM   1671  H8  DMS   108      16.804  17.251  19.418   0.080   1.484
+ATOM   1672  H9  DMS   108      17.964  16.332  18.728   0.080   1.484
+ATOM   1673  H10 DMS   108      18.069  17.960  18.670   0.080   1.484
+TER
+END

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/FKBP/dss-min.pqr

@@ -0,0 +1,14 @@
+ATOM   1664  S   DSS   108      18.252  17.192  20.920   0.349   1.996
+ATOM   1665  O   DSS   108      17.730  16.166  21.890  -0.541   1.658
+ATOM   1666  C1  DSS   108      17.418  16.962  19.356   0.004   1.904
+ATOM   1667  C2  DSS   108      17.541  18.705  21.324  -0.359   1.904
+ATOM   1668  S3  DSS   108      18.085  20.050  20.263  -0.190   1.996
+ATOM   1669  C4  DSS   108      17.631  21.458  21.373  -0.168   1.904
+ATOM   1670  H7  DSS   108      16.429  16.942  19.505   0.052   1.484
+ATOM   1671  H8  DSS   108      17.711  16.099  18.946   0.052   1.484
+ATOM   1672  H9  DSS   108      17.646  17.717  18.742   0.052   1.484
+ATOM   1673  H10 DSS   108      17.781  18.947  22.264   0.220   1.484
+ATOM   1674  H11 DSS   108      16.546  18.639  21.242   0.220   1.484
+ATOM   1675  H12 DSS   108      16.647  21.438  21.553   0.103   1.484
+ATOM   1676  H13 DSS   108      17.870  22.323  20.931   0.103   1.484
+ATOM   1677  H14 DSS   108      18.129  21.377  22.236   0.103   1.484

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/README.md

@@ -0,0 +1,32 @@
+# APBS version validation and test cases
+
+## APBS examples and test cases
+
+This directory serves as the root directory for the APBS test suite.
+In each directory you will find example input files to use with APBS and a README file displaying the results for different versions of APBS.
+
+Executing <code>make test</code> in each directory will run the examples for that directory and log the results to <code>TESTRESULTS.log</code>.
+Executing <code>make test</code> from the root examples directory will run all the tests listed below.
+Tests will either pass, pass with rounding error (within 10<sup>-9</sup> of the expected result), or fail outright.
+
+| Example | README file | Source | Description | 
+| ---- | ---- | ---- | ---- | 
+| Actin dimer (actin-dimer) | [actin-dimer/README.md](actin-dimer/README.md) | Dave Sept | Calculate binding energies for actin dimers. This is an example of a large biomolecule binding energy calculation that often requires parallel focusing. | 
+| Alkane nonpolar solvation energies (alkanes) | [alkanes/README.md](alkanes/README.md) | Nathan Baker, Jason Wagoner | Calculate nonpolar solvation energies for various alkanes.  Taken from Wagoner JA, Baker NA. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. [Proc Natl Acad Sci USA, 103, 8331-8336, 2006.](http://dx.doi.org/10.1073/pnas.0600118103) |
+| Born ion (born) | [born/README.md](born/README.md) | Nathan Baker | Calculate solvation energies for ions of various sizes and compare to the analytical results. |
+| FKBP (FKBP) | [FKBP/README.md](FKBP/README.md) | Jung-Hsin Lin | Binding of various (small) ligands to FKBP.  Analogous to HCA binding case (except it works). |
+| HCA ligand binding (hca-bind) | [hca-bind/README.md](hca-bind/README.md) | UHBD | Calculate the binding of a small molecule (acetazolamide) to a medium-sized protein (human carbonic anhydrase). |
+| Acetic acid ionization (ionize) | [ionize/README.md](ionize/README.md) | UHBD | Calculate electrostatic contributions to the ionization energy of acetic acid. | 
+| Ion-ion PMF (ion-pmf) | [ion-pmf/README.md](ion-pmf/README.md) | Nathan Baker | Calculate solvation energies and solvation force components for ion pairs. |
+| Ion-protein interaction energies (ion-protein) | [ion-protein/README.md](ion-protein/README.md) | Dave Sept | Calculate polar energy of placing an ion near a macromolecule. |
+| PKA-balanol binding (pka-lig) | [pka-lig/README.md](pka-lig/README.md) | Chung Wong | Calculate binding energies of a ligand to protein kinase A. |
+| PKA-balanol binding (pka-lig)/UHDB | [pka-lig/UHDB/readme.md](pka-lig/UHDB/readme.md)| Chun Wong | Shows the calculations done using molecular surface based and van der Waals dielectric definitions. |
+| Coulomb's law (point-pmf) | [point-pmf/README.md](point-pmf/README.md) | Nathan Baker | See how well we do reproducing Coulomb's law. |
+| Methanol solvation (solv) | [solv/README.md](solv/README.md) | UHBD | Calculate the solvation energies of methanol and methoxide. | 
+| Protein-RNA interactions (protein-rna) | [protein-rna/README.md](protein-rna/README.md) | David Draper | Calculate the salt dependence of protein interactions with box B RNA hairpin. |
+| Geometric flow solvation model | [geoflow/README.md](geoflow/README.md) | Elizabeth Jurrus | Calculate the dielectric interface profile across the solute-solvent boundary in a thermodynamically sef-consistent fashion. |
+| Ion Binding to DNA Duplexes Using SMPBE| [smpbe/readme.md](smpbe/reamdme.md) | | Calculate PBE taking into account the finite ion size. |
+| Focusing Membrane Boundary Condition| [membrane/readme.md](membrane/readme.md) | | Solve the PBE with a single atom using focusing membrane boundary conditions. |
+| NMR Structure of the RNA binding Domain | [bem/readme.md](bem/readme.md) | | Calculate the solvation complex using the boundary element method as is implemented in APBS. |
+| Born Ion | [opal/README.md](opal/README.md) | Nathan Baker | The Born ion is a canonical electrostatic's test case for which there is an analytical solution. This example examines the solvation free energy. |
+| Miscellaneous | [misc/README.md](misc/README.md) | | A collection of pqr files of molecules that have interesting potentials. |

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/actin-dimer/README.md

@@ -0,0 +1,117 @@
+README for Actin-Dimer APBS examples
+====================================
+
+The example input files in this directory calculate binding energies for actin dimers. This is an example of a large biomolecule binding energy calculation that often requires parallel focusing.
+
+This example was contributed by Dave Sept.
+
+Input File                          | Description | APBS Version | Results (kJ/mol) | UHBD (kJ/mol)
+------------------------------------|-------------|--------------|------------------|--------------
+[apbs-mol-auto.in](apbs-mol-auto.in)| Sequential, 2-level focusing to ≤ 0.725 A, NPBE, srfm mol| **3.0** | **104.868** | 106.7 (1.00 A res., NPBE)
+| | |1.5 | 104.868 |
+| | |1.4.2 |104.868
+| | |1.4.1 |104.8683
+| | |1.4   |104.8683
+| | |1.3 | 104.8683<sup>[8](#8)</sup>
+| | |1.2.1 | 104.867
+| | |1.2 |104.867
+| | |1.1.0 |104.867<sup>[5](#5)</sup>
+| | |1.0.0 |104.868
+| | |0.5.1 |104.868<sup>[3](#3)</sup>
+| | |0.5.0 | 105.0338<sup>[2](#2)</sup>
+| | |0.4.0 |104.8895
+[apbs-smol-auto.in](apbs-smol-auto.in) | Sequential, 2-level focusing to ≤ 0.725 A, NPBE, srfm smol | **3.0** | **109.5841** | 106.7 (1.00 A res., NPBE)
+| | |1.5   |109.5841
+| | |1.4.2 |109.5841
+| | |1.4.1 |109.5841
+| | |1.4   |109.5841
+| | |1.3   |109.5841<sup>[8](#8)</sup>
+| | |1.2.1 |109.5829
+| | |1.2   |109.5829
+| | |1.1.0 |109.5829<sup>[5](#5)</sup>
+| | |1.0.0 |109.5841
+| | |0.5.1 |109.5841<sup>[3](#3)</sup>
+| | |0.5.0 |109.7518<sup>[2](#2)</sup>
+| | |0.4.0 |109.6043<sup>[1](#1)</sup>
+| | |0.3.2 |90.8704
+| | |0.3.1 |88.6101
+| | |0.3.0 |88.6101
+| | |0.2.6 |88.6101
+| | |0.2.5 |88.6101
+| | |0.2.4 |88.6101
+| | |0.2.3 |88.6064
+| | |0.2.2 |90.829
+| | |0.2.1 |90.829
+| | |0.2.0 |90.829
+| | |0.1.8 |90.84
+[apbs-mol-parallel.in](apbs-mol-parallel.in) |Parallel with 8 processors, focusing to \~0.9 A, LPBE, srfm mol |**1.5**|**98.1746**|106.7 (1.00 A res., NPBE)
+| | |1.4.2 |98.1746
+| | |1.4.1 |98.1746
+| | |1.4   |98.1746
+| | |1.3   |98.1746<sup>[8](#8)</sup>
+| | |1.2.1 |98.1733<sup>[7](#7)</sup>
+| | |1.2   |98.1635<sup>[6](#6)</sup>
+| | |1.1.0 |98.1630<sup>[5](#5)</sup>
+| | |1.0.0 |98.1643<sup>[4](#4)</sup>
+| | |0.5.1 |98.1654<sup>[3](#3)</sup>
+| | |0.5.0 |98.3530<sup>[2](#2)</sup>
+| | |0.4.0 |98.1834
+[apbs-smol-parallel.in](apbs-smol-parallel.in)|Parallel with 8 processors, focusing to \~0.9 A, LPBE, srfm smol|**1.5**|**115.542**|106.7 (1.00 A res., NPBE)
+| | |1.4.2 |115.542
+| | |1.4.1 |115.5421
+| | |1.4   |115.5421<sup>[9](#9)</sup>
+| | |1.3   |115.5422<sup>[8](#8)</sup>
+| | |1.2.1 |115.5409<sup>[7](#7)</sup>
+| | |1.2   |115.5563<sup>[6](#6)</sup>
+| | |1.1.0 |115.5560<sup>[5](#5)</sup>
+| | |1.0.0 |115.5573<sup>[4](#4)</sup>
+| | |0.5.1 |115.5584<sup>[3](#3)</sup>
+| | |0.5.0 |115.7492<sup>[2](#2)</sup>
+| | |0.4.0 |115.5751<sup>[1](#1)</sup>
+| | |0.3.2 |87.1121
+| | |0.3.1 |87.1121
+| | |0.3.0 |90.2573
+| | |0.2.6 |90.2573
+| | |0.2.5 |90.2573
+| | |0.2.4 |90.2573
+| | |0.2.3 |90.2543
+| | |0.2.2 |91.9450
+| | |0.2.1 |91.945
+| | |0.2.0 |91.939
+| | |0.1.8 |91.67
+
+<a name=1></a><sup>1</sup> The discrepancy in values between versions 0.4.0 and 0.3.2 is most likely due to three factors:
+
+-   A bug fix in Vacc\_molAcc which removed spurious regions of high internal dielectric values
+-   A switch in the algorithm used to compute the dielectric smoothing for srfm smol.
+-   The addition of the Vacc sphere density (sdens keyword) as a variable and a change in the default sdens value from 3.0 to 10.0
+
+<a name=2></a><sup>2</sup> The discrepancy in values between versions 0.5.0 and 0.4.0 is most likely due to the following factor(s):
+
+-   A change in the autofocusing routine for APBS
+
+<a name=3></a><sup>3</sup> The discrepancy in values between versions 0.5.1 and 0.5.0 is most likely due to the following factor(s):
+
+-   Bug fix regarding multipole behavior for neutral proteins
+
+<a name=4></a><sup>4</sup> The discrepancy in values between versions 0.5.1 and 1.0.0 was due to the execution of the previous APBS tests on a PowerPC platform with the XLC/XLF compilers. Running with binaries compiled with gcc/gfortran or the Intel compilers gives identical results between versions 0.5.1 and 1.0.0.
+
+<a name=5></a><sup>5</sup> The discrepancy in values between versions 1.0.0 and 1.1.0 is due to a bugfix in the implementation of the boundary conditions. This bug introduces a very small error (generally less than 1%) the calculated results.
+
+<a name=6></a><sup>6</sup> APBS 1.2 has switched the multigrid smoothing algorithm from standard Gauss-Seidel to Gauss-Seidel red/black in order to facilitate parallelization. This switch has caused small differences in individual calculation energies which, when combined to the final answer, create larger errors (up to 0.04%). These errors can be reduced by resetting the APBS error tolerance to 1e-9 or smaller values. For a more detailed explanation, please see the FAQ, [here](http://www.poissonboltzmann.org/docs/apbs-faq/#sources error calculation).
+
+<a name=7></a><sup>7</sup> The discrepancy in values between versions 1.2 and 1.2.1 is most likely due to the following factor(s):
+
+-   Fixed a bug in Vpmg\_fillcoCoefMolIon which causes npbe based calculations to return very large energies
+
+<a name=8></a><sup>8</sup> The discrepancy in values between versions 1.2.1 and 1.3 is most likely due to the following factor(s):
+
+-   Fixed a bug in Vpmg.c which causes zero potential values on boundaries in non-focusing calculations.
+
+<a name=9></a><sup>9</sup> The discrepancy in values between versions 1.3 and 1.4 is most likely due to the following factor(s):
+
+-   Translation of contrib/pmgZ library from FORTRAN to C
+-   Differences in numerical implementations between FORTRAN and C compilers result in small round-off discrepencies
+-   Small margins due to these round-off discrepencies acumulate in the computations
+
+Please see the ChangeLog or the [APBS website](http://www.poissonboltzmann.org/) for more information.

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/actin-dimer/UHBD/aheall-atom.charmm.dat

@@ -0,0 +1,762 @@
+CHARMM23
+! all-atom charges and radii 
+resi  atom   chrg   epsi   sigm   radi end
+!
+ALA   N    -0.47   0.000  0.000  1.850
+ALA   HN    0.31   0.000  0.000  1.00
+ALA   CA    0.07   0.000  0.000  2.275
+ALA   HA    0.09   0.000  0.000  1.32
+ALA   CB   -0.27   0.000  0.000  2.06
+ALA   HB1   0.09   0.000  0.000  1.32
+ALA   HB2   0.09   0.000  0.000  1.32
+ALA   HB3   0.09   0.000  0.000  1.32
+ALA   C     0.51   0.000  0.000  2.00
+ALA   O    -0.51   0.000  0.000  1.70 
+!
+ARG   N    -0.47   0.000  0.000  1.850
+ARG   HN    0.31   0.000  0.000  1.00
+ARG   CA    0.07   0.000  0.000  2.275
+ARG   HA    0.09   0.000  0.000  1.32
+ARG   CB   -0.18   0.000  0.000  2.175
+ARG   HB1   0.09   0.000  0.000  1.32
+ARG   HB2   0.09   0.000  0.000  1.32
+ARG   CG   -0.18   0.000  0.000  2.175
+ARG   HG1   0.09   0.000  0.000  1.32
+ARG   HG2   0.09   0.000  0.000  1.32
+ARG   CD    0.20   0.000  0.000  2.175
+ARG   HD1   0.09   0.000  0.000  1.32
+ARG   HD2   0.09   0.000  0.000  1.32
+ARG   NE   -0.70   0.000  0.000  1.85
+ARG   HE    0.44   0.000  0.000  1.00
+ARG   CZ    0.64   0.000  0.000  2.00
+ARG   NH1  -0.80   0.000  0.000  1.85
+ARG   HH11  0.46   0.000  0.000  1.00
+ARG   HH12  0.46   0.000  0.000  1.00
+ARG   NH2  -0.80   0.000  0.000  1.85
+ARG   HH21  0.46   0.000  0.000  1.00
+ARG   HH22  0.46   0.000  0.000  1.00
+ARG   C     0.51   0.000  0.000  2.00
+ARG   O    -0.51   0.000  0.000  1.70 
+!
+ASN   N    -0.47   0.000  0.000  1.850
+ASN   HN    0.31   0.000  0.000  1.00
+ASN   CA    0.07   0.000  0.000  2.275
+ASN   HA    0.09   0.000  0.000  1.32
+ASN   CB   -0.18   0.000  0.000  2.175
+ASN   HB1   0.09   0.000  0.000  1.32
+ASN   HB2   0.09   0.000  0.000  1.32
+ASN   CG    0.55   0.000  0.000  2.00
+ASN   OD1  -0.55   0.000  0.000  1.70
+ASN   ND2  -0.62   0.000  0.000  1.85
+ASN   HD21  0.32   0.000  0.000  1.00
+ASN   HD22  0.30   0.000  0.000  1.00
+ASN   C     0.51   0.000  0.000  2.00
+ASN   O    -0.51   0.000  0.000  1.70 
+!
+ASP   N    -0.47   0.000  0.000  1.850
+ASP   HN    0.31   0.000  0.000  1.00
+ASP   CA    0.07   0.000  0.000  2.275
+ASP   HA    0.09   0.000  0.000  1.32
+ASP   CB   -0.28   0.000  0.000  2.175
+ASP   HB1   0.09   0.000  0.000  1.32
+ASP   HB2   0.09   0.000  0.000  1.32
+ASP   CG    0.62   0.000  0.000  2.00
+ASP   OD1  -0.76   0.000  0.000  1.70
+ASP   OD2  -0.76   0.000  0.000  1.70
+ASP   C     0.51   0.000  0.000  2.00
+ASP   O    -0.51   0.000  0.000  1.70  
+!
+ASY   N    -0.47   0.000  0.000  1.850
+ASY   HN    0.31   0.000  0.000  1.00
+ASY   CA    0.07   0.000  0.000  2.275
+ASY   HA    0.09   0.000  0.000  1.32
+ASY   CB   -0.28   0.000  0.000  2.175
+ASY   HB1   0.09   0.000  0.000  1.32
+ASY   HB2   0.09   0.000  0.000  1.32
+ASY   CG    0.62   0.000  0.000  2.00
+ASY   OD1  -0.76   0.000  0.000  1.70
+ASY   OD2  -0.76   0.000  0.000  1.70
+ASY   C     0.51   0.000  0.000  2.00
+ASY   O    -0.51   0.000  0.000  1.70
+ASY   CAY  -0.27   0.000  0.000  2.175
+ASY   HY1   0.09   0.000  0.000  1.32
+ASY   HY2   0.09   0.000  0.000  1.32
+ASY   HY3   0.09   0.000  0.000  1.32
+ASY   CY    0.51   0.000  0.000  2.00
+ASY   OY   -0.51   0.000  0.000  1.70
+!
+CA    CA    2.00   0.000  0.000  1.811
+!
+CYS   N    -0.47   0.000  0.000  1.850
+CYS   HN    0.31   0.000  0.000  1.00
+CYS   CA    0.07   0.000  0.000  2.275
+CYS   HA    0.09   0.000  0.000  1.32
+CYS   CB   -0.11   0.000  0.000  2.175
+CYS   HB1   0.09   0.000  0.000  1.32
+CYS   HB2   0.09   0.000  0.000  1.32
+CYS   SG   -0.23   0.000  0.000  2.000
+CYS   HG1   0.16   0.000  0.000  1.00
+CYS   C     0.51   0.000  0.000  2.00
+CYS   O    -0.51   0.000  0.000  1.70  
+!
+CYX   N    -0.47   0.000  0.000  1.850
+CYX   HN    0.31   0.000  0.000  1.00
+CYX   CA    0.07   0.000  0.000  2.275
+CYX   HA    0.09   0.000  0.000  1.32
+CYX   CB   -0.10   0.000  0.000  2.175
+CYX   HB1   0.09   0.000  0.000  1.32
+CYX   HB2   0.09   0.000  0.000  1.32
+CYX   SG   -0.08   0.000  0.000  2.000
+CYX   C     0.51   0.000  0.000  2.00
+CYX   O    -0.51   0.000  0.000  1.70  
+!
+FES   FE1  -0.020  0.000  0.000  2.000 
+FES   FE2  -0.020  0.000  0.000  2.000 
+FES   S1   -0.420  0.000  0.000  2.000 
+FES   S2   -0.420  0.000  0.000  2.000 
+!
+GLN   N    -0.47   0.000  0.000  1.850
+GLN   HN    0.31   0.000  0.000  1.00
+GLN   CA    0.07   0.000  0.000  2.275
+GLN   HA    0.09   0.000  0.000  1.32
+GLN   CB   -0.18   0.000  0.000  2.175
+GLN   HB1   0.09   0.000  0.000  1.32
+GLN   HB2   0.09   0.000  0.000  1.32
+GLN   CG   -0.18   0.000  0.000  2.175
+GLN   HG1   0.09   0.000  0.000  1.32
+GLN   HG2   0.09   0.000  0.000  1.32
+GLN   CD    0.55   0.000  0.000  2.00
+GLN   OE1  -0.55   0.000  0.000  1.70
+GLN   NE2  -0.62   0.000  0.000  1.85
+GLN   HE21  0.32   0.000  0.000  1.00
+GLN   HE22  0.30   0.000  0.000  1.00
+GLN   C     0.51   0.000  0.000  2.00
+GLN   O    -0.51   0.000  0.000  1.70  
+!
+GLU   N    -0.47   0.000  0.000  1.850
+GLU   HN    0.31   0.000  0.000  1.00
+GLU   CA    0.07   0.000  0.000  2.275
+GLU   HA    0.09   0.000  0.000  1.32
+GLU   CB   -0.18   0.000  0.000  2.175
+GLU   HB1   0.09   0.000  0.000  1.32
+GLU   HB2   0.09   0.000  0.000  1.32
+GLU   CG   -0.28   0.000  0.000  2.175
+GLU   HG1   0.09   0.000  0.000  1.32
+GLU   HG2   0.09   0.000  0.000  1.32
+GLU   CD    0.62   0.000  0.000  2.00
+GLU   OE1  -0.76   0.000  0.000  1.70
+GLU   OE2  -0.76   0.000  0.000  1.70
+GLU   C     0.51   0.000  0.000  2.00
+GLU   O    -0.51   0.000  0.000  1.70
+!
+GLY   N    -0.47   0.000  0.000  1.850
+GLY   HN    0.31   0.000  0.000  1.00
+GLY   CA   -0.02   0.000  0.000  2.275
+GLY   HA1   0.09   0.000  0.000  1.32
+GLY   HA2   0.09   0.000  0.000  1.32
+GLY   C     0.51   0.000  0.000  2.00
+GLY   O    -0.51   0.000  0.000  1.70
+!
+HSD   N    -0.47   0.000  0.000  1.850
+HSD   HN    0.31   0.000  0.000  1.00
+HSD   CA    0.07   0.000  0.000  2.275
+HSD   HA    0.09   0.000  0.000  1.32
+HSD   ND1  -0.36   0.000  0.000  1.85
+HSD   HD1   0.32   0.000  0.000  1.00
+HSD   CG   -0.05   0.000  0.000  1.80
+HSD   CB   -0.09   0.000  0.000  2.175
+HSD   HB1   0.09   0.000  0.000  1.32
+HSD   HB2   0.09   0.000  0.000  1.32
+HSD   NE2  -0.70   0.000  0.000  1.85
+HSD   CD2   0.22   0.000  0.000  1.80
+HSD   HD2   0.10   0.000  0.000  1.468
+HSD   CE1   0.25   0.000  0.000  1.80
+HSD   HE1   0.13   0.000  0.000  0.90
+HSD   C     0.51   0.000  0.000  2.00
+HSD   O    -0.51   0.000  0.000  1.70
+!
+HSE   N    -0.47   0.000  0.000  1.850
+HSE   HN    0.31   0.000  0.000  1.00
+HSE   CA    0.07   0.000  0.000  2.275
+HSE   HA    0.09   0.000  0.000  1.32
+HSE   NE2  -0.36   0.000  0.000  1.85
+HSE   HE2   0.32   0.000  0.000  1.00
+HSE   CD2  -0.05   0.000  0.000  1.80
+HSE   HD2   0.09   0.000  0.000  1.468 
+HSE   ND1  -0.70   0.000  0.000  1.85
+HSE   CG    0.22   0.000  0.000  1.80
+HSE   CE1   0.25   0.000  0.000  1.80
+HSE   HE1   0.13   0.000  0.000  0.90
+HSE   CB   -0.08   0.000  0.000  2.175
+HSE   HB1   0.09   0.000  0.000  1.32
+HSE   HB2   0.09   0.000  0.000  1.32
+HSE   C     0.51   0.000  0.000  2.00
+HSE   O    -0.51   0.000  0.000  1.70
+!
+HSP   N    -0.47   0.000  0.000  1.850
+HSP   HN    0.31   0.000  0.000  1.00
+HSP   CA    0.07   0.000  0.000  2.275
+HSP   HA    0.09   0.000  0.000  1.32
+HSP   ND1  -0.51   0.000  0.000  1.85
+HSP   HD1   0.44   0.000  0.000  1.00
+HSP   NE2  -0.51   0.000  0.000  1.85
+HSP   HE2   0.44   0.000  0.000  1.00
+HSP   CE1   0.32   0.000  0.000  1.80
+HSP   HE1   0.18   0.000  0.000  0.70
+HSP   CD2   0.19   0.000  0.000  1.80
+HSP   HD2   0.13   0.000  0.000  0.90
+HSP   CG    0.19   0.000  0.000  1.80
+HSP   CB   -0.05   0.000  0.000  2.175
+HSP   HB1   0.09   0.000  0.000  1.32
+HSP   HB2   0.09   0.000  0.000  1.32
+HSP   C     0.51   0.000  0.000  2.00
+HSP   O    -0.51   0.000  0.000  1.70
+!
+HMS   N    -0.47   0.000  0.000  1.850
+HMS   HN    0.31   0.000  0.000  1.00
+HMS   CA    0.07   0.000  0.000  2.275
+HMS   HA    0.09   0.000  0.000  1.32
+HMS   ND1  -0.51   0.000  0.000  1.85
+HMS   HD1   0.44   0.000  0.000  1.00
+HMS   NE2  -0.51   0.000  0.000  1.85
+HMS   CM    0.17   0.000  0.000  2.175
+HMS   HM1   0.09   0.000  0.000  1.32
+HMS   HM2   0.09   0.000  0.000  1.32
+HMS   HM3   0.09   0.000  0.000  1.32
+HMS   CE1   0.32   0.000  0.000  1.80
+HMS   HE1   0.18   0.000  0.000  0.70
+HMS   CD2   0.19   0.000  0.000  1.80
+HMS   HD2   0.13   0.000  0.000  0.90
+HMS   CG    0.19   0.000  0.000  1.80
+HMS   CB   -0.05   0.000  0.000  2.175
+HMS   HB1   0.09   0.000  0.000  1.32
+HMS   HB2   0.09   0.000  0.000  1.32
+HMS   C     0.51   0.000  0.000  2.00
+HMS   O    -0.51   0.000  0.000  1.70
+!
+ILE   N    -0.47   0.000  0.000  1.850
+ILE   HN    0.31   0.000  0.000  1.00
+ILE   CA    0.07   0.000  0.000  2.275
+ILE   HA    0.09   0.000  0.000  1.32
+ILE   CB   -0.09   0.000  0.000  2.275
+ILE   HB    0.09   0.000  0.000  1.32
+ILE   CG2  -0.27   0.000  0.000  2.06
+ILE   HG21  0.09   0.000  0.000  1.32
+ILE   HG22  0.09   0.000  0.000  1.32
+ILE   HG23  0.09   0.000  0.000  1.32
+ILE   CG1  -0.18   0.000  0.000  2.175
+ILE   HG11  0.09   0.000  0.000  1.32
+ILE   HG12  0.09   0.000  0.000  1.32
+ILE   CD   -0.27   0.000  0.000  2.06
+ILE   HD1   0.09   0.000  0.000  1.32
+ILE   HD2   0.09   0.000  0.000  1.32
+ILE   HD3   0.09   0.000  0.000  1.32
+ILE   C     0.51   0.000  0.000  2.00
+ILE   O    -0.51   0.000  0.000  1.70
+!
+LEU   N    -0.47   0.000  0.000  1.850
+LEU   HN    0.31   0.000  0.000  1.00
+LEU   CA    0.07   0.000  0.000  2.275
+LEU   HA    0.09   0.000  0.000  1.32
+LEU   CB   -0.18   0.000  0.000  2.175
+LEU   HB1   0.09   0.000  0.000  1.32
+LEU   HB2   0.09   0.000  0.000  1.32
+LEU   CG   -0.09   0.000  0.000  2.275
+LEU   HG    0.09   0.000  0.000  1.32
+LEU   CD1  -0.27   0.000  0.000  2.06
+LEU   HD11  0.09   0.000  0.000  1.32
+LEU   HD12  0.09   0.000  0.000  1.32
+LEU   HD13  0.09   0.000  0.000  1.32
+LEU   CD2  -0.27   0.000  0.000  2.06
+LEU   HD21  0.09   0.000  0.000  1.32
+LEU   HD22  0.09   0.000  0.000  1.32
+LEU   HD23  0.09   0.000  0.000  1.32
+LEU   C     0.51   0.000  0.000  2.00
+LEU   O    -0.51   0.000  0.000  1.70
+!
+LYS   N    -0.47   0.000  0.000  1.850
+LYS   HN    0.31   0.000  0.000  1.00
+LYS   CA    0.07   0.000  0.000  2.275
+LYS   HA    0.09   0.000  0.000  1.32
+LYS   CB   -0.18   0.000  0.000  2.175
+LYS   HB1   0.09   0.000  0.000  1.32
+LYS   HB2   0.09   0.000  0.000  1.32
+LYS   CG   -0.18   0.000  0.000  2.175
+LYS   HG1   0.09   0.000  0.000  1.32
+LYS   HG2   0.09   0.000  0.000  1.32
+LYS   CD   -0.18   0.000  0.000  2.175
+LYS   HD1   0.09   0.000  0.000  1.32
+LYS   HD2   0.09   0.000  0.000  1.32
+LYS   CE    0.21   0.000  0.000  2.175
+LYS   HE1   0.05   0.000  0.000  1.32
+LYS   HE2   0.05   0.000  0.000  1.32
+LYS   NZ   -0.30   0.000  0.000  1.85
+LYS   HZ1   0.33   0.000  0.000  1.00
+LYS   HZ2   0.33   0.000  0.000  1.00
+LYS   HZ3   0.33   0.000  0.000  1.00
+LYS   C     0.51   0.000  0.000  2.00
+LYS   O    -0.51   0.000  0.000  1.70
+!
+MET   N    -0.47   0.000  0.000  1.850
+MET   HN    0.31   0.000  0.000  1.00
+MET   CA    0.07   0.000  0.000  2.275
+MET   HA    0.09   0.000  0.000  1.32
+MET   CB   -0.18   0.000  0.000  2.175
+MET   HB1   0.09   0.000  0.000  1.32
+MET   HB2   0.09   0.000  0.000  1.32
+MET   CG   -0.14   0.000  0.000  2.175
+MET   HG1   0.09   0.000  0.000  1.32
+MET   HG2   0.09   0.000  0.000  1.32
+MET   SD   -0.09   0.000  0.000  2.00
+MET   CE   -0.22   0.000  0.000  2.06
+MET   HE1   0.09   0.000  0.000  1.32
+MET   HE2   0.09   0.000  0.000  1.32
+MET   HE3   0.09   0.000  0.000  1.32
+MET   C     0.51   0.000  0.000  2.00
+MET   O    -0.51   0.000  0.000  1.70
+!
+PHE   N    -0.47   0.000  0.000  1.850
+PHE   HN    0.31   0.000  0.000  1.00
+PHE   CA    0.07   0.000  0.000  2.275
+PHE   HA    0.09   0.000  0.000  1.32
+PHE   CB   -0.18   0.000  0.000  2.175
+PHE   HB1   0.09   0.000  0.000  1.32
+PHE   HB2   0.09   0.000  0.000  1.32
+PHE   CG    0.000  0.000  0.000  1.9924
+PHE   CD1  -0.115  0.000  0.000  1.9924
+PHE   HD1   0.115  0.000  0.000  1.3582
+PHE   CD2  -0.115  0.000  0.000  1.9924
+PHE   HD2   0.115  0.000  0.000  1.3582
+PHE   CE1  -0.115  0.000  0.000  1.9924
+PHE   HE1   0.115  0.000  0.000  1.3582
+PHE   CE2  -0.115  0.000  0.000  1.9924
+PHE   HE2   0.115  0.000  0.000  1.3582
+PHE   CZ   -0.115  0.000  0.000  1.9924
+PHE   HZ    0.115  0.000  0.000  1.3582
+PHE   C     0.51   0.000  0.000  2.00
+PHE   O    -0.51   0.000  0.000  1.70
+!
+PRO   N    -0.29   0.000  0.000  1.85
+PRO   CA    0.02   0.000  0.000  2.275
+PRO   HA    0.09   0.000  0.000  1.32
+PRO   CD    0.00   0.000  0.000  2.175
+PRO   HD1   0.09   0.000  0.000  1.32
+PRO   HD2   0.09   0.000  0.000  1.32
+PRO   CB   -0.18   0.000  0.000  2.175
+PRO   HB1   0.09   0.000  0.000  1.32
+PRO   HB2   0.09   0.000  0.000  1.32
+PRO   CG   -0.18   0.000  0.000  2.175
+PRO   HG1   0.09   0.000  0.000  1.32 
+PRO   HG2   0.09   0.000  0.000  1.32
+PRO   C     0.51   0.000  0.000  2.0
+PRO   O    -0.51   0.000  0.000  1.7
+!
+PRON  N    -0.07   0.000  0.000  1.85
+PRON  HN1   0.24   0.000  0.000  1.00
+PRON  HN2   0.24   0.000  0.000  1.00
+PRON  CD    0.16   0.000  0.000  2.175
+PRON  CA    0.16   0.000  0.000  2.275
+PRON  HA    0.09   0.000  0.000  1.32
+PRON  HD1   0.09   0.000  0.000  1.32
+PRON  HD2   0.09   0.000  0.000  1.32
+!
+SER   N    -0.47   0.000  0.000  1.850
+SER   HN    0.31   0.000  0.000  1.00
+SER   CA    0.07   0.000  0.000  2.275
+SER   HA    0.09   0.000  0.000  1.32
+SER   CB    0.05   0.000  0.000  2.175
+SER   HB1   0.09   0.000  0.000  1.32
+SER   HB2   0.09   0.000  0.000  1.32
+SER   OG   -0.66   0.000  0.000  1.77
+SER   HG1   0.43   0.000  0.000  1.00 
+SER   C     0.51   0.000  0.000  2.00
+SER   O    -0.51   0.000  0.000  1.70
+!
+THR   N    -0.47   0.000  0.000  1.850
+THR   HN    0.31   0.000  0.000  1.00
+THR   CA    0.07   0.000  0.000  2.275
+THR   HA    0.09   0.000  0.000  1.32
+THR   CB    0.14   0.000  0.000  2.175
+THR   HB    0.09   0.000  0.000  1.32
+THR   OG1  -0.66   0.000  0.000  1.77
+THR   HG1   0.43   0.000  0.000  1.00   
+THR   CG2  -0.27   0.000  0.000  2.06
+THR   HG21  0.09   0.000  0.000  1.32
+THR   HG22  0.09   0.000  0.000  1.32
+THR   HG23  0.09   0.000  0.000  1.32
+THR   C     0.51   0.000  0.000  2.00
+THR   O    -0.51   0.000  0.000  1.70
+!
+TRP   N    -0.47   0.000  0.000  1.850
+TRP   HN    0.31   0.000  0.000  1.00
+TRP   CA    0.07   0.000  0.000  2.275
+TRP   HA    0.09   0.000  0.000  1.32
+TRP   CB   -0.18   0.000  0.000  2.175
+TRP   HB1   0.09   0.000  0.000  1.32
+TRP   HB2   0.09   0.000  0.000  1.32
+TRP   CG   -0.03   0.000  0.000  1.9924
+TRP   CD2  -0.02   0.000  0.000  1.8
+TRP   CD1   0.035  0.000  0.000  1.9924
+TRP   HD1   0.115  0.000  0.000  1.3582
+TRP   NE1  -0.61   0.000  0.000  1.85
+TRP   HE1   0.38   0.000  0.000  1.00
+TRP   CE2   0.13   0.000  0.000  1.8
+TRP   CE3  -0.115  0.000  0.000  1.9924
+TRP   HE3   0.115  0.000  0.000  1.3582
+TRP   CZ2  -0.115  0.000  0.000  1.9924 
+TRP   HZ2   0.115  0.000  0.000  1.3582
+TRP   CZ3  -0.115  0.000  0.000  1.9924
+TRP   HZ3   0.115  0.000  0.000  1.3582
+TRP   CH2  -0.115  0.000  0.000  1.9924
+TRP   HH2   0.115  0.000  0.000  1.3582
+TRP   C     0.51   0.000  0.000  2.00
+TRP   O    -0.51   0.000  0.000  1.70
+!
+TYR   N    -0.47   0.000  0.000  1.850
+TYR   HN    0.31   0.000  0.000  1.00
+TYR   CA    0.07   0.000  0.000  2.275
+TYR   HA    0.09   0.000  0.000  1.32
+TYR   CB   -0.18   0.000  0.000  2.175
+TYR   HB1   0.09   0.000  0.000  1.32
+TYR   HB2   0.09   0.000  0.000  1.32
+TYR   CG    0.00   0.000  0.000  1.9924
+TYR   CD1  -0.115  0.000  0.000  1.9924
+TYR   HD1   0.115  0.000  0.000  1.3582
+TYR   CD2  -0.115  0.000  0.000  1.9924
+TYR   HD2   0.115  0.000  0.000  1.3582
+TYR   CE1  -0.115  0.000  0.000  1.9924
+TYR   HE1   0.115  0.000  0.000  1.3582
+TYR   CE2  -0.115  0.000  0.000  1.9924
+TYR   HE2   0.115  0.000  0.000  1.3582
+TYR   CZ    0.11   0.000  0.000  1.9924
+TYR   OH   -0.54   0.000  0.000  1.77
+TYR   HH    0.43   0.000  0.000  1.00
+TYR   C     0.51   0.000  0.000  2.00
+TYR   O    -0.51   0.000  0.000  1.70
+!
+VAL   N    -0.47   0.000  0.000  1.850
+VAL   HN    0.31   0.000  0.000  1.00
+VAL   CA    0.07   0.000  0.000  2.275
+VAL   HA    0.09   0.000  0.000  1.32
+VAL   CB   -0.09   0.000  0.000  2.175
+VAL   HB    0.09   0.000  0.000  1.32
+VAL   CG1  -0.27   0.000  0.000  2.06
+VAL   HG11  0.09   0.000  0.000  1.32
+VAL   HG12  0.09   0.000  0.000  1.32
+VAL   HG13  0.09   0.000  0.000  1.32
+VAL   CG2  -0.27   0.000  0.000  2.06
+VAL   HG21  0.09   0.000  0.000  1.32
+VAL   HG22  0.09   0.000  0.000  1.32
+VAL   HG23  0.09   0.000  0.000  1.32
+VAL   C     0.51   0.000  0.000  2.00
+VAL   O    -0.51   0.000  0.000  1.70
+! 
+NTE   N    -0.30   0.000  0.000  1.85
+NTE   HT1   0.33   0.000  0.000  1.32
+NTE   HT2   0.33   0.000  0.000  1.32
+NTE   HT3   0.33   0.000  0.000  1.32
+NTE   CA    0.21   0.000  0.000  2.275
+NTE   HA    0.10   0.000  0.000  1.32
+! 
+CTE   C     0.34   0.000  0.000  2.00
+CTE   OT1  -0.67   0.000  0.000  1.70
+CTE   OT2  -0.67   0.000  0.000  1.70
+!
+GUA   P     1.50   0.000  0.000  2.15
+GUA   O1P  -0.80   0.000  0.000  1.70
+GUA   O2P  -0.80   0.000  0.000  1.70
+GUA   O5'  -0.55   0.000  0.000  1.77
+GUA   C5'  -0.08   0.000  0.000  2.175
+GUA   H5'   0.09   0.000  0.000  1.32
+GUA   H5''  0.09   0.000  0.000  1.32
+GUA   C4'   0.11   0.000  0.000  2.275
+GUA   H4'   0.09   0.000  0.000  1.32
+GUA   O4'  -0.40   0.000  0.000  1.77
+GUA   C1'   0.11   0.000  0.000  2.275
+GUA   H1'   0.09   0.000  0.000  1.32
+GUA   N9   -0.14   0.000  0.000  1.85
+GUA   C4    0.14   0.000  0.000  1.80
+GUA   N3   -0.66   0.000  0.000  1.85
+GUA   C2    0.76   0.000  0.000  1.80
+GUA   N1   -0.38   0.000  0.000  1.85
+GUA   H1    0.28   0.000  0.000  1.00
+GUA   N2   -0.64   0.000  0.000  1.85
+GUA   H21   0.31   0.000  0.000  1.00
+GUA   H22   0.33   0.000  0.000  1.00
+GUA   C6    0.55   0.000  0.000  1.80
+GUA   O6   -0.47   0.000  0.000  1.70
+GUA   C5   -0.08   0.000  0.000  1.80
+GUA   N7   -0.69   0.000  0.000  1.85
+GUA   C8    0.41   0.000  0.000  1.80
+GUA   H8    0.28   0.000  0.000  1.32
+GUA   O2'  -0.66   0.000  0.000  1.77
+GUA   C3'   0.01   0.000  0.000  2.275
+GUA   H3'   0.09   0.000  0.000  1.32
+GUA   O3'  -0.55   0.000  0.000  1.77
+!
+! Note that above is true for RIBOSE - the following parameters should
+! be used to overwrite the above it DEOXYRIBOSE is wanted
+!
+!GUA   C2'   0.14   0.000  0.000  2.275
+!GUA   H2'   0.43   0.000  0.000  1.00
+!GUA   H2''  0.09   0.000  0.000  1.32
+!
+GUA   C2'  -0.18   0.000  0.000  2.175
+GUA   H2'   0.09   0.000  0.000  1.32
+GUA   H2''  0.09   0.000  0.000  1.32
+!
+ADP   PA    1.30   0.000  0.000  2.15
+ADP   O1PA -0.80   0.000  0.000  1.70
+ADP   O2PA -0.80   0.000  0.000  1.70
+ADP   O5'  -0.60   0.000  0.000  1.77
+ADP   C5'  -0.08   0.000  0.000  2.175
+ADP   H5'   0.09   0.000  0.000  1.32
+ADP   H5''  0.09   0.000  0.000  1.32
+ADP   C4'   0.11   0.000  0.000  2.275
+ADP   H4'   0.09   0.000  0.000  1.32
+ADP   O4'  -0.40   0.000  0.000  1.77
+ADP   C1'   0.11   0.000  0.000  2.275
+ADP   H1'   0.09   0.000  0.000  1.32
+ADP   C5    0.23   0.000  0.000  1.80
+ADP   N7   -0.63   0.000  0.000  1.85
+ADP   C8    0.38   0.000  0.000  1.80
+ADP   H8    0.18   0.000  0.000  1.32
+ADP   N9   -0.16   0.000  0.000  1.85
+ADP   N1   -0.74   0.000  0.000  1.85
+ADP   C2    0.53   0.000  0.000  1.80
+ADP   H2    0.16   0.000  0.000  1.32
+ADP   N3   -0.69   0.000  0.000  1.85
+ADP   C4    0.31   0.000  0.000  1.80
+ADP   C6    0.43   0.000  0.000  1.80
+ADP   N6   -0.80   0.000  0.000  1.85
+ADP   H61   0.40   0.000  0.000  1.00
+ADP   H62   0.40   0.000  0.000  1.00
+ADP   C2'   0.14   0.000  0.000  2.175
+ADP   H2''  0.09   0.000  0.000  1.32
+ADP   O2'  -0.66   0.000  0.000  1.77
+ADP   H2'   0.43   0.000  0.000  1.32
+ADP   C3'   0.14   0.000  0.000  2.275
+ADP   H3'   0.09   0.000  0.000  1.32
+ADP   O3'  -0.66   0.000  0.000  1.77
+ADP   H3T   0.43   0.000  0.000  1.32
+ADP   OLIN -0.80   0.000  0.000  1.70
+ADP   PB    1.30   0.000  0.000  2.15
+ADP   O1PB -0.90   0.000  0.000  1.70
+ADP   O2PB -0.90   0.000  0.000  1.70
+ADP   O3PB -0.90   0.000  0.000  1.70
+!
+ATP   PG    1.20   0.000  0.000  2.15
+ATP   O1PG -1.00   0.000  0.000  1.70
+ATP   O2PG -1.00   0.000  0.000  1.70
+ATP   O3PG -1.00   0.000  0.000  1.70
+ATP   PB    1.30   0.000  0.000  2.15
+ATP   O1PB -0.70   0.000  0.000  1.70
+ATP   O2PB -0.70   0.000  0.000  1.70
+ATP   O3PA -0.70   0.000  0.000  1.70
+ATP   PA    1.30   0.000  0.000  2.15
+ATP   O1PA -0.70   0.000  0.000  1.70
+ATP   O2PA -0.70   0.000  0.000  1.70
+ATP   O5'  -0.60   0.000  0.000  1.77
+ATP   C5'  -0.08   0.000  0.000  2.175
+ATP   H5'   0.09   0.000  0.000  1.32
+ATP   H5''  0.09   0.000  0.000  1.32
+ATP   C4'   0.11   0.000  0.000  2.275
+ATP   H4'   0.09   0.000  0.000  1.32
+ATP   O4'  -0.40   0.000  0.000  1.77
+ATP   C1'   0.11   0.000  0.000  2.275
+ATP   H1'   0.09   0.000  0.000  1.32
+ATP   C5    0.23   0.000  0.000  1.80
+ATP   N7   -0.63   0.000  0.000  1.85
+ATP   C8    0.38   0.000  0.000  1.80
+ATP   H8    0.18   0.000  0.000  1.32
+ATP   N9   -0.16   0.000  0.000  1.85
+ATP   N1   -0.74   0.000  0.000  1.85
+ATP   C2    0.53   0.000  0.000  1.80
+ATP   H2    0.16   0.000  0.000  1.32
+ATP   N3   -0.69   0.000  0.000  1.85
+ATP   C4    0.31   0.000  0.000  1.80
+ATP   C6    0.43   0.000  0.000  1.80
+ATP   N6   -0.80   0.000  0.000  1.85
+ATP   H61   0.40   0.000  0.000  1.00
+ATP   H62   0.40   0.000  0.000  1.00
+ATP   C2'   0.14   0.000  0.000  2.175
+ATP   H2''  0.09   0.000  0.000  1.32
+ATP   O2'  -0.66   0.000  0.000  1.77
+ATP   H2'   0.43   0.000  0.000  1.32
+ATP   C3'   0.14   0.000  0.000  2.275
+ATP   H3'   0.09   0.000  0.000  1.32
+ATP   O3'  -0.66   0.000  0.000  1.77
+ATP   H3T   0.43   0.000  0.000  1.32
+ATP   OLIN -0.80   0.000  0.000  1.70
+
+!
+ADE   P     1.50   0.000  0.000  2.15
+ADE   O1P  -0.80   0.000  0.000  1.70
+ADE   O2P  -0.80   0.000  0.000  1.70
+ADE   O5'  -0.55   0.000  0.000  1.77
+ADE   C5'  -0.08   0.000  0.000  2.175
+ADE   H5'   0.09   0.000  0.000  1.32
+ADE   H5''  0.09   0.000  0.000  1.32
+ADE   C4'   0.11   0.000  0.000  2.275
+ADE   H4'   0.09   0.000  0.000  1.32
+ADE   O4'  -0.40   0.000  0.000  1.77
+ADE   C1'   0.11   0.000  0.000  2.275
+ADE   H1'   0.09   0.000  0.000  1.32
+ADE   C5    0.23   0.000  0.000  1.80
+ADE   N7   -0.63   0.000  0.000  1.85
+ADE   C8    0.38   0.000  0.000  1.80
+ADE   H8    0.18   0.000  0.000  1.32
+ADE   N9   -0.16   0.000  0.000  1.85
+ADE   N1   -0.74   0.000  0.000  1.85
+ADE   C2    0.53   0.000  0.000  1.80
+ADE   H2    0.16   0.000  0.000  1.32
+ADE   N3   -0.69   0.000  0.000  1.85
+ADE   C4    0.31   0.000  0.000  1.80
+ADE   C6    0.43   0.000  0.000  1.80
+ADE   N6   -0.80   0.000  0.000  1.85
+ADE   H61   0.40   0.000  0.000  1.00
+ADE   H62   0.40   0.000  0.000  1.00
+ADE   O2'  -0.66   0.000  0.000  1.77
+ADE   C3'   0.01   0.000  0.000  2.275
+ADE   H3'   0.09   0.000  0.000  1.32
+ADE   O3'  -0.55   0.000  0.000  1.77
+!
+! Note that above is true for RIBOSE - the following parameters should
+! be used to overwrite the above it DEOXYRIBOSE is wanted
+!
+!ADE   C2'   0.14   0.000  0.000  2.275
+!ADE   H2'   0.43   0.000  0.000  1.00
+!ADE   H2''  0.09   0.000  0.000  1.32
+ADE   C2'  -0.18   0.000  0.000  2.175
+ADE   H2'   0.09   0.000  0.000  1.32
+ADE   H2''  0.09   0.000  0.000  1.32
+!
+CYT   P     1.50   0.000  0.000  2.15
+CYT   O1P  -0.80   0.000  0.000  1.70
+CYT   O2P  -0.80   0.000  0.000  1.70
+CYT   O5'  -0.55   0.000  0.000  1.77
+CYT   C5'  -0.08   0.000  0.000  2.175
+CYT   H5'   0.09   0.000  0.000  1.32
+CYT   H5''  0.09   0.000  0.000  1.32
+CYT   C4'   0.11   0.000  0.000  2.275
+CYT   H4'   0.09   0.000  0.000  1.32
+CYT   O4'  -0.40   0.000  0.000  1.77
+CYT   C1'   0.11   0.000  0.000  2.275
+CYT   H1'   0.09   0.000  0.000  1.32
+CYT   N1   -0.16   0.000  0.000  1.85
+CYT   C6    0.11   0.000  0.000  1.80
+CYT   H6    0.05   0.000  0.000  1.32
+CYT   C2    0.53   0.000  0.000  1.80
+CYT   O2   -0.48   0.000  0.000  1.70
+CYT   N3   -0.67   0.000  0.000  1.85
+CYT   C4    0.62   0.000  0.000  1.80
+CYT   N4   -0.58   0.000  0.000  1.85
+CYT   H41   0.31   0.000  0.000  1.00
+CYT   H42   0.27   0.000  0.000  1.00
+CYT   C5   -0.10   0.000  0.000  1.80
+CYT   H5    0.10   0.000  0.000  1.32
+CYT   O2'  -0.66   0.000  0.000  1.77
+CYT   C3'   0.01   0.000  0.000  2.275
+CYT   H3'   0.09   0.000  0.000  1.32
+CYT   O3'  -0.55   0.000  0.000  1.77
+!
+! Note that above is true for RIBOSE - the following parameters should
+! be used to overwrite the above it DEOXYRIBOSE is wanted
+!
+!CYT   C2'   0.14   0.000  0.000  2.275
+!CYT   H2'   0.43   0.000  0.000  1.00
+!CYT   H2''  0.09   0.000  0.000  1.32
+CYT   C2'  -0.18   0.000  0.000  2.175
+CYT   H2'   0.09   0.000  0.000  1.32
+CYT   H2''  0.09   0.000  0.000  1.32
+!
+THY   P     1.50   0.000  0.000  2.15
+THY   O1P  -0.80   0.000  0.000  1.70
+THY   O2P  -0.80   0.000  0.000  1.70
+THY   O5'  -0.55   0.000  0.000  1.77
+THY   C5'  -0.08   0.000  0.000  2.175
+THY   H5'   0.09   0.000  0.000  1.32
+THY   H5''  0.09   0.000  0.000  1.32
+THY   C4'   0.11   0.000  0.000  2.275
+THY   H4'   0.09   0.000  0.000  1.32
+THY   O4'  -0.40   0.000  0.000  1.77
+THY   C1'   0.11   0.000  0.000  2.275
+THY   H1'   0.09   0.000  0.000  1.32
+THY   N1   -0.30   0.000  0.000  1.85
+THY   C6    0.17   0.000  0.000  1.80
+THY   H6    0.13   0.000  0.000  1.32
+THY   C2    0.57   0.000  0.000  1.80
+THY   O2   -0.47   0.000  0.000  1.70
+THY   N3   -0.46   0.000  0.000  1.85
+THY   H3    0.36   0.000  0.000  1.00
+THY   C4    0.54   0.000  0.000  1.80
+THY   O4   -0.49   0.000  0.000  1.70
+THY   C5   -0.15   0.000  0.000  1.80
+THY   C5M  -0.11   0.000  0.000  2.06
+THY   H51   0.07   0.000  0.000  1.32
+THY   H52   0.07   0.000  0.000  1.32
+THY   H53   0.07   0.000  0.000  1.32
+THY   O2'  -0.66   0.000  0.000  1.77
+THY   C3'   0.01   0.000  0.000  2.275
+THY   H3'   0.09   0.000  0.000  1.32
+THY   O3'  -0.55   0.000  0.000  1.77
+!
+! Note that above is true for RIBOSE - the following parameters should
+! be used to overwrite the above it DEOXYRIBOSE is wanted
+!
+!THY   C2'   0.14   0.000  0.000  2.275
+!THY   H2'   0.43   0.000  0.000  1.00
+!THY   H2''  0.09   0.000  0.000  1.32
+THY   C2'  -0.18   0.000  0.000  2.175
+THY   H2'   0.09   0.000  0.000  1.32
+THY   H2''  0.09   0.000  0.000  1.32
+!
+TE5   H5T   0.43   0.000  0.000  1.00
+TE5   O5'  -0.66   0.000  0.000  1.77
+TE5   C5'   0.05   0.000  0.000  2.175
+TE5   H5'   0.09   0.000  0.000  1.32
+TE5   H5''  0.09   0.000  0.000  1.32
+!
+TE3   C3'   0.14   0.000  0.000  2.275
+TE3   H3'   0.09   0.000  0.000  1.32
+TE3   O3'  -0.66   0.000  0.000  1.77
+TE3   H3T   0.43   0.000  0.000  1.00
+!
+!
+CMP   P     1.50   0.000  0.000  2.15
+CMP   O1P  -0.80   0.000  0.000  1.70
+CMP   O2P  -0.80   0.000  0.000  1.70
+CMP   O5'  -0.55   0.000  0.000  1.77
+CMP   C5'  -0.08   0.000  0.000  2.175
+CMP   H5'   0.09   0.000  0.000  1.32
+CMP   H5''  0.09   0.000  0.000  1.32
+CMP   C4'   0.11   0.000  0.000  2.275
+CMP   H4'   0.09   0.000  0.000  1.32
+CMP   O4'  -0.40   0.000  0.000  1.77
+CMP   C1'   0.11   0.000  0.000  2.275
+CMP   H1'   0.09   0.000  0.000  1.32
+CMP   C5    0.23   0.000  0.000  1.80
+CMP   N7   -0.63   0.000  0.000  1.85
+CMP   C8    0.38   0.000  0.000  1.80
+CMP   H8    0.18   0.000  0.000  1.32
+CMP   N9   -0.16   0.000  0.000  1.85
+CMP   N1   -0.74   0.000  0.000  1.85
+CMP   C2    0.53   0.000  0.000  1.80
+CMP   H2    0.16   0.000  0.000  1.32
+CMP   N3   -0.69   0.000  0.000  1.85
+CMP   C4    0.31   0.000  0.000  1.80
+CMP   C6    0.43   0.000  0.000  1.80
+CMP   N6   -0.80   0.000  0.000  1.85
+CMP   H61   0.40   0.000  0.000  1.00
+CMP   H62   0.40   0.000  0.000  1.00
+CMP   O2'  -0.66   0.000  0.000  1.77
+CMP   C3'   0.01   0.000  0.000  2.275
+CMP   H3'   0.09   0.000  0.000  1.32
+CMP   O3'  -0.55   0.000  0.000  1.77
+!
+! Note that above is true for RIBOSE - the following parameters should
+! be used to overwrite the above it DEOXYRIBOSE is wanted
+!
+CMP   C2'   0.14   0.000  0.000  2.275
+CMP   H2T   0.43   0.000  0.000  1.00
+CMP   H2'   0.09   0.000  0.000  1.32

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.inp

@@ -0,0 +1,85 @@
+read                   ! read
+    mol 1              ! molecule 1
+    file 'prot3.pdb'      ! from pdb file
+    pdb                ! in free-format PDB format
+end
+read                   ! read
+    mol 2              ! molecule 1
+    file 'prot4.pdb'      ! from pdb file
+    pdb                ! in free-format PDB format
+end
+set
+    charge             ! the charges
+    radii              ! and the radii
+    param CHARMM23        ! using parameter set "amber"
+    file 'aheall-atom.charmm.dat'     ! from the file "ahe.dat"
+end
+
+elec                   ! calculate the electrostatic potential
+    calc
+    dime 200 200 200 
+    grid 1.00           ! using a grid spacing of 1.0 Angstroms
+    all 
+    ions 50.0 
+    full
+    maxits 500
+    pdie  2.0
+    nsph 200
+    sdie 78.4
+    rion 2.0
+    nmap 1.4           ! use probe-accessible surface
+    bcfl 2             ! using boundary condition 2
+    gcent   2.821 -0.073 0.815 
+end
+print elec zenerg all end
+print elec energy all end
+print elec self   all end
+print elec fdcoul all end
+print elec tenerg all end
+
+elec                   ! calculate the electrostatic potential
+    calc
+    dime 200 200 200
+    grid 1.00           ! using a grid spacing of 1.0 Angstroms
+    mol 1  
+    full
+    ions 50.0
+    maxits 500
+    pdie  2.0
+    nsph 200
+    sdie 78.4
+    rion 2.0
+    nmap 1.4           ! use probe-accessible surface
+    bcfl 2             ! using boundary condition 2
+    gcent   2.821 -0.073 0.815
+end
+print elec zenerg mol 1 end
+print elec energy mol 1 end
+print elec self   mol 1 end
+print elec fdcoul mol 1 end
+print elec tenerg mol 1 end
+
+elec                   ! calculate the electrostatic potential
+    calc
+    dime 200 200 200
+    grid 1.00           ! using a grid spacing of 1.0 Angstroms
+    mol 2  
+    full
+    ions 50.0
+    maxits 500
+    pdie  2.0
+    nsph 200
+    sdie 78.4
+    rion 2.0
+    nmap 1.4           ! use probe-accessible surface
+    bcfl 2             ! using boundary condition 2
+    gcent   2.821 -0.073 0.815
+end
+print elec zenerg mol 2 end
+print elec energy mol 2 end
+print elec self   mol 2 end
+print elec fdcoul mol 2 end
+print elec tenerg mol 2 end
+
+stop
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/actin-dimer/UHBD/single.inp

@@ -0,0 +1,32 @@
+read                   ! read
+    mol 1              ! molecule 1
+    file 'prot3.pdb'      ! from pdb file
+    pdb                ! in free-format PDB format
+end
+read                   ! read
+    mol 2              ! molecule 1
+    file 'prot4.pdb'      ! from pdb file
+    pdb                ! in free-format PDB format
+end
+set
+    charge             ! the charges
+    radii              ! and the radii
+    param CHARMM23        ! using parameter set "amber"
+    file 'aheall-atom.charmm.dat'     ! from the file "ahe.dat"
+end
+
+elec                   ! calculate the electrostatic potential
+    calc
+    dime 97 97 97 
+    grid 1.5           ! using a grid spacing of 1.0 Angstroms
+    all 
+    ions 50.0 
+    maxits 500
+    pdie  2.0
+    nsph 200
+    sdie 78.4
+    rion 2.0
+    nmap 1.4           ! use probe-accessible surface
+    bcfl 1             ! using boundary condition 2
+    gcent   2.821 -0.073 0.815 
+end

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/actin-dimer/apbs-mol-auto.in

@@ -0,0 +1,89 @@
+##########################################################################
+# ACTIN DIMER BINDING ENERGY
+##########################################################################
+
+read 
+    mol pqr mol1.pqr
+    mol pqr mol2.pqr
+    mol pqr complex.pqr
+end
+
+# CALCULATE POTENTIAL FOR FIRST COMPONENT 
+elec name mol1
+    mg-auto
+    dime  161 161 161
+    cglen 156 121 162
+    fglen 112  91 116
+    cgcent mol 3
+    fgcent mol 3
+    mol 1
+    npbe
+    bcfl sdh
+    ion charge 1 conc 0.050 radius 2.0
+    ion charge -1 conc 0.050 radius 2.0
+    pdie 2.0
+    sdie 78.4
+    srfm mol
+    chgm spl0
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# CALCULATE POTENTIAL FOR SECOND COMPONENT
+elec name mol2
+    mg-auto
+    dime  161 161 161
+    cglen 156 121 162
+    fglen 112  91 116
+    cgcent mol 3
+    fgcent mol 3
+    mol 2
+    npbe
+    bcfl sdh
+    ion charge 1 conc 0.050 radius 2.0
+    ion charge -1 conc 0.050 radius 2.0
+    pdie 2.0
+    sdie 78.4
+    srfm mol
+    chgm spl0
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15 
+    calcenergy total
+    calcforce no
+end
+
+# CALCULATE POTENTIAL FOR COMPLEX
+elec name complex
+    mg-auto
+    dime  161 161 161
+    cglen 156 121 162
+    fglen 112  91 116
+    cgcent mol 3
+    fgcent mol 3
+    mol 3
+    npbe
+    bcfl sdh
+    ion charge 1 conc 0.050 radius 2.0
+    ion charge -1 conc 0.050 radius 2.0
+    pdie 2.0
+    sdie 78.4
+    srfm mol
+    chgm spl0
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# COMBINE TO GIVE BINDING ENERGY
+print elecEnergy complex - mol2 - mol1 end
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/actin-dimer/apbs-mol-auto.out

@@ -0,0 +1,261 @@
+
+
+----------------------------------------------------------------------
+    APBS -- Adaptive Poisson-Boltzmann Solver
+    Version APBS 3.4.1
+    
+    Nathan A. Baker (nathan.baker@pnnl.gov)
+    Pacific Northwest National Laboratory
+    
+    Additional contributing authors listed in the code documentation.
+    
+    Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
+    Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
+    Northwest Division for the U.S. Department of Energy.
+    
+    Portions Copyright (c) 2002-2010, Washington University in St. Louis.
+    Portions Copyright (c) 2002-2020, Nathan A. Baker.
+    Portions Copyright (c) 1999-2002, The Regents of the University of California.
+    Portions Copyright (c) 1995, Michael Holst.
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+    
+    * Redistributions of source code must retain the above copyright notice, this
+      list of conditions and the following disclaimer.
+    
+    * Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+    
+    * Neither the name of the developer nor the names of its contributors may be
+      used to endorse or promote products derived from this software without
+      specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+    ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+    ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+    (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+    LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+    ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+----------------------------------------------------------------------
+    APBS uses FETK (the Finite Element ToolKit) to solve the
+    Poisson-Boltzmann equation numerically.  FETK is a portable collection
+    of finite element modeling class libraries developed by the Michael Holst
+    research group and written in an object-oriented form of C.  FEtk is
+    designed to solve general coupled systems of nonlinear partial differential
+    equations using adaptive finite element methods, inexact Newton methods,
+    and algebraic multilevel methods.  More information about FEtk may be found
+    at <http://www.FEtk.ORG>.
+----------------------------------------------------------------------
+    APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
+    Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
+    which has been modified by Patrice Koehl
+    <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
+    memory usage when solving the Poisson-Boltzmann equation.
+----------------------------------------------------------------------
+    Please cite your use of APBS as:
+
+    Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
+    nanosystems: application to microtubules and the ribosome. Proc.
+    Natl. Acad. Sci. USA 98, 10037-10041 2001.
+    
+
+This executable compiled on Apr 29 2022 at 19:42:46
+
+Parsing input file apbs-mol-auto.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from mol1.pqr.
+  5877 atoms
+  Centered at (1.535e+01, -3.100e-02, 2.993e+00)
+  Net charge -1.20e+01 e
+Reading PQR-format atom data from mol2.pqr.
+  5877 atoms
+  Centered at (-1.404e+01, -3.356e+00, 3.049e+01)
+  Net charge -1.20e+01 e
+Reading PQR-format atom data from complex.pqr.
+  11754 atoms
+  Centered at (2.518e+00, -2.465e+00, 1.674e+01)
+  Net charge -2.40e+01 e
+Preparing to run 6 PBE calculations.
+----------------------------------------
+CALCULATION #1 (mol1): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  13.5959 A
+  Current memory usage:  1028.322 MB total, 1028.322 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 161 x 161 x 161
+  Grid spacings: 0.975 x 0.756 x 1.012
+  Grid lengths: 156.000 x 121.000 x 162.000
+  Grid center: (2.518, -2.465, 16.742)
+  Multigrid levels: 4
+  Molecule ID: 1
+  Nonlinear traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.050 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.050 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.050 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.400
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.527617850342E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #2 (mol1): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  13.5959 A
+  Current memory usage:  1028.322 MB total, 2042.113 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 161 x 161 x 161
+  Grid spacings: 0.700 x 0.569 x 0.725
+  Grid lengths: 112.000 x 91.000 x 116.000
+  Grid center: (2.518, -2.465, 16.742)
+  Multigrid levels: 4
+  Molecule ID: 1
+  Nonlinear traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.050 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.050 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.050 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.400
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 2.919510754196E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (mol2): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  13.5959 A
+  Current memory usage:  1030.291 MB total, 2042.113 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 161 x 161 x 161
+  Grid spacings: 0.975 x 0.756 x 1.012
+  Grid lengths: 156.000 x 121.000 x 162.000
+  Grid center: (2.518, -2.465, 16.742)
+  Multigrid levels: 4
+  Molecule ID: 2
+  Nonlinear traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.050 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.050 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.050 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.400
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.527671844880E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #4 (mol2): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  13.5959 A
+  Current memory usage:  1030.291 MB total, 2046.048 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 161 x 161 x 161
+  Grid spacings: 0.700 x 0.569 x 0.725
+  Grid lengths: 112.000 x 91.000 x 116.000
+  Grid center: (2.518, -2.465, 16.742)
+  Multigrid levels: 4
+  Molecule ID: 2
+  Nonlinear traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.050 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.050 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.050 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.400
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 2.915468859278E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #5 (complex): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  13.5959 A
+  Current memory usage:  1046.446 MB total, 2046.048 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 161 x 161 x 161
+  Grid spacings: 0.975 x 0.756 x 1.012
+  Grid lengths: 156.000 x 121.000 x 162.000
+  Grid center: (2.518, -2.465, 16.742)
+  Multigrid levels: 4
+  Molecule ID: 3
+  Nonlinear traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.050 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.050 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.050 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.400
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 3.056317807611E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #6 (complex): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  13.5959 A
+  Current memory usage:  1046.446 MB total, 2069.492 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 161 x 161 x 161
+  Grid spacings: 0.700 x 0.569 x 0.725
+  Grid lengths: 112.000 x 91.000 x 116.000
+  Grid center: (2.518, -2.465, 16.742)
+  Multigrid levels: 4
+  Molecule ID: 3
+  Nonlinear traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.050 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.050 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.050 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.400
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 5.836028296532E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 3 (complex) - 2 (mol2) - 1 (mol1) end
+  Local net energy (PE 0) = 1.048683058625E+02 kJ/mol
+  Global net ELEC energy = 1.048683058625E+02 kJ/mol
+----------------------------------------
+CLEANING UP AND SHUTTING DOWN...
+Destroying force arrays.
+No energy arrays to destroy.
+Destroying multigrid structures.
+Destroying finite element structures.
+Destroying 3 molecules
+Final memory usage:  0.001 MB total, 2069.492 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/actin-dimer/apbs-mol-parallel.in

@@ -0,0 +1,96 @@
+#########################################################################/smo
+# ACTIN DIMER BINDING ENERGY
+##########################################################################
+
+read
+    mol pqr mol1.pqr
+    mol pqr mol2.pqr
+    mol pqr complex.pqr
+end
+
+# CALCULATE POTENTIAL FOR COMPONENT 1
+elec name mol1
+    mg-para
+    ofrac 0.1
+    pdime 2 2 2
+    dime  97  97  97
+    fglen 112 91 116
+    cglen 156 121 162
+    cgcent mol 3
+    fgcent mol 3
+    mol 1
+    npbe
+    bcfl sdh
+    ion charge 1 conc 0.050 radius 2.0
+    ion charge -1 conc 0.050 radius 2.0
+    pdie 2.0
+    sdie 78.54
+    srfm mol
+    chgm spl0
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# CALCULATE POTENTIAL FOR COMPONENT 2
+elec name mol2
+    mg-para
+    ofrac 0.1
+    pdime 2 2 2
+    dime  97  97  97
+    fglen 112 91 116
+    cglen 156 121 162
+    cgcent mol 3
+    fgcent mol 3
+    mol 2
+    npbe
+    bcfl sdh
+    ion charge 1 conc 0.050 radius 2.0
+    ion charge -1 conc 0.050 radius 2.0
+    pdie 2.0
+    sdie 78.54
+    srfm mol
+    chgm spl0
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# CALCULATE POTENTIAL FOR COMPLEX
+elec name complex
+    mg-para
+    ofrac 0.1
+    pdime 2 2 2
+    dime  97  97  97
+    fglen 112 91 116
+    cglen 156 121 162
+    cgcent mol 3
+    fgcent mol 3
+    mol 3
+    npbe
+    bcfl sdh
+    ion charge 1 conc 0.050 radius 2.0
+    ion charge -1 conc 0.050 radius 2.0
+    pdie 2.0
+    sdie 78.54
+    srfm mol
+    chgm spl0
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+    write pot dx pot
+end
+
+# COMBINE TO GIVE BINDING ENERGY
+print elecEnergy complex - mol1 - mol2 end
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/actin-dimer/apbs-smol-auto.in

@@ -0,0 +1,89 @@
+##########################################################################
+# ACTIN DIMER BINDING ENERGY
+##########################################################################
+
+read 
+    mol pqr mol1.pqr
+    mol pqr mol2.pqr
+    mol pqr complex.pqr
+end
+
+# CALCULATE POTENTIAL FOR FIRST COMPONENT 
+elec name mol1
+    mg-auto
+    dime  161 161 161
+    cglen 156 121 162
+    fglen 112  91 116
+    cgcent mol 3
+    fgcent mol 3
+    mol 1
+    npbe
+    bcfl sdh
+    ion charge 1 conc 0.050 radius 2.0
+    ion charge -1 conc 0.050 radius 2.0
+    pdie 2.0
+    sdie 78.4
+    srfm smol
+    chgm spl0
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# CALCULATE POTENTIAL FOR SECOND COMPONENT
+elec name mol2
+    mg-auto
+    dime  161 161 161
+    cglen 156 121 162
+    fglen 112  91 116
+    cgcent mol 3
+    fgcent mol 3
+    mol 2
+    npbe
+    bcfl sdh
+    ion charge 1 conc 0.050 radius 2.0
+    ion charge -1 conc 0.050 radius 2.0
+    pdie 2.0
+    sdie 78.4
+    srfm smol
+    chgm spl0
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15 
+    calcenergy total
+    calcforce no
+end
+
+# CALCULATE POTENTIAL FOR COMPLEX
+elec name complex
+    mg-auto
+    dime  161 161 161
+    cglen 156 121 162
+    fglen 112  91 116
+    cgcent mol 3
+    fgcent mol 3
+    mol 3
+    npbe
+    bcfl sdh
+    ion charge 1 conc 0.050 radius 2.0
+    ion charge -1 conc 0.050 radius 2.0
+    pdie 2.0
+    sdie 78.4
+    srfm smol
+    chgm spl0
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# COMBINE TO GIVE BINDING ENERGY
+print elecEnergy complex - mol2 - mol1 end
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/actin-dimer/apbs-smol-auto.out

@@ -0,0 +1,261 @@
+
+
+----------------------------------------------------------------------
+    APBS -- Adaptive Poisson-Boltzmann Solver
+    Version APBS 3.4.1
+    
+    Nathan A. Baker (nathan.baker@pnnl.gov)
+    Pacific Northwest National Laboratory
+    
+    Additional contributing authors listed in the code documentation.
+    
+    Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
+    Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
+    Northwest Division for the U.S. Department of Energy.
+    
+    Portions Copyright (c) 2002-2010, Washington University in St. Louis.
+    Portions Copyright (c) 2002-2020, Nathan A. Baker.
+    Portions Copyright (c) 1999-2002, The Regents of the University of California.
+    Portions Copyright (c) 1995, Michael Holst.
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+    
+    * Redistributions of source code must retain the above copyright notice, this
+      list of conditions and the following disclaimer.
+    
+    * Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+    
+    * Neither the name of the developer nor the names of its contributors may be
+      used to endorse or promote products derived from this software without
+      specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+    ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+    ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+    (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+    LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+    ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+----------------------------------------------------------------------
+    APBS uses FETK (the Finite Element ToolKit) to solve the
+    Poisson-Boltzmann equation numerically.  FETK is a portable collection
+    of finite element modeling class libraries developed by the Michael Holst
+    research group and written in an object-oriented form of C.  FEtk is
+    designed to solve general coupled systems of nonlinear partial differential
+    equations using adaptive finite element methods, inexact Newton methods,
+    and algebraic multilevel methods.  More information about FEtk may be found
+    at <http://www.FEtk.ORG>.
+----------------------------------------------------------------------
+    APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
+    Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
+    which has been modified by Patrice Koehl
+    <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
+    memory usage when solving the Poisson-Boltzmann equation.
+----------------------------------------------------------------------
+    Please cite your use of APBS as:
+
+    Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
+    nanosystems: application to microtubules and the ribosome. Proc.
+    Natl. Acad. Sci. USA 98, 10037-10041 2001.
+    
+
+This executable compiled on Apr 29 2022 at 19:42:46
+
+Parsing input file apbs-smol-auto.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from mol1.pqr.
+  5877 atoms
+  Centered at (1.535e+01, -3.100e-02, 2.993e+00)
+  Net charge -1.20e+01 e
+Reading PQR-format atom data from mol2.pqr.
+  5877 atoms
+  Centered at (-1.404e+01, -3.356e+00, 3.049e+01)
+  Net charge -1.20e+01 e
+Reading PQR-format atom data from complex.pqr.
+  11754 atoms
+  Centered at (2.518e+00, -2.465e+00, 1.674e+01)
+  Net charge -2.40e+01 e
+Preparing to run 6 PBE calculations.
+----------------------------------------
+CALCULATION #1 (mol1): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  13.5959 A
+  Current memory usage:  1028.322 MB total, 1028.322 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 161 x 161 x 161
+  Grid spacings: 0.975 x 0.756 x 1.012
+  Grid lengths: 156.000 x 121.000 x 162.000
+  Grid center: (2.518, -2.465, 16.742)
+  Multigrid levels: 4
+  Molecule ID: 1
+  Nonlinear traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.050 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.050 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.050 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.400
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.528632421825E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #2 (mol1): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  13.5959 A
+  Current memory usage:  1028.322 MB total, 2042.113 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 161 x 161 x 161
+  Grid spacings: 0.700 x 0.569 x 0.725
+  Grid lengths: 112.000 x 91.000 x 116.000
+  Grid center: (2.518, -2.465, 16.742)
+  Multigrid levels: 4
+  Molecule ID: 1
+  Nonlinear traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.050 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.050 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.050 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.400
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 2.920618662320E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (mol2): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  13.5959 A
+  Current memory usage:  1030.291 MB total, 2042.113 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 161 x 161 x 161
+  Grid spacings: 0.975 x 0.756 x 1.012
+  Grid lengths: 156.000 x 121.000 x 162.000
+  Grid center: (2.518, -2.465, 16.742)
+  Multigrid levels: 4
+  Molecule ID: 2
+  Nonlinear traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.050 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.050 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.050 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.400
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.529297900572E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #4 (mol2): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  13.5959 A
+  Current memory usage:  1030.291 MB total, 2046.048 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 161 x 161 x 161
+  Grid spacings: 0.700 x 0.569 x 0.725
+  Grid lengths: 112.000 x 91.000 x 116.000
+  Grid center: (2.518, -2.465, 16.742)
+  Multigrid levels: 4
+  Molecule ID: 2
+  Nonlinear traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.050 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.050 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.050 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.400
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 2.916592202835E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #5 (complex): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  13.5959 A
+  Current memory usage:  1046.446 MB total, 2046.048 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 161 x 161 x 161
+  Grid spacings: 0.975 x 0.756 x 1.012
+  Grid lengths: 156.000 x 121.000 x 162.000
+  Grid center: (2.518, -2.465, 16.742)
+  Multigrid levels: 4
+  Molecule ID: 3
+  Nonlinear traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.050 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.050 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.050 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.400
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 3.059244262535E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #6 (complex): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  13.5959 A
+  Current memory usage:  1046.446 MB total, 2069.492 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 161 x 161 x 161
+  Grid spacings: 0.700 x 0.569 x 0.725
+  Grid lengths: 112.000 x 91.000 x 116.000
+  Grid center: (2.518, -2.465, 16.742)
+  Multigrid levels: 4
+  Molecule ID: 3
+  Nonlinear traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.050 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.050 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.050 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.400
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 5.838306706232E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 3 (complex) - 2 (mol2) - 1 (mol1) end
+  Local net energy (PE 0) = 1.095841077691E+02 kJ/mol
+  Global net ELEC energy = 1.095841077691E+02 kJ/mol
+----------------------------------------
+CLEANING UP AND SHUTTING DOWN...
+Destroying force arrays.
+No energy arrays to destroy.
+Destroying multigrid structures.
+Destroying finite element structures.
+Destroying 3 molecules
+Final memory usage:  0.001 MB total, 2069.492 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/actin-dimer/apbs-smol-parallel.in

@@ -0,0 +1,96 @@
+##########################################################################
+# ACTIN DIMER BINDING ENERGY
+##########################################################################
+
+read 
+    mol pqr mol1.pqr
+    mol pqr mol2.pqr
+    mol pqr complex.pqr
+end
+
+# CALCULATE POTENTIAL FOR COMPONENT 1
+elec name mol1
+    mg-para
+    ofrac 0.1
+    pdime 2 2 2
+    dime  97  97  97
+    fglen 112 91 116
+    cglen 156 121 162
+    cgcent mol 3
+    fgcent mol 3
+    mol 1
+    npbe
+    bcfl sdh
+    ion charge 1 conc 0.050 radius 2.0
+    ion charge -1 conc 0.050 radius 2.0
+    pdie 2.0
+    sdie 78.54
+    srfm smol
+    chgm spl0
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# CALCULATE POTENTIAL FOR COMPONENT 2
+elec name mol2
+    mg-para
+    ofrac 0.1
+    pdime 2 2 2
+    dime  97  97  97
+    fglen 112 91 116
+    cglen 156 121 162
+    cgcent mol 3
+    fgcent mol 3
+    mol 2
+    npbe
+    bcfl sdh
+    ion charge 1 conc 0.050 radius 2.0
+    ion charge -1 conc 0.050 radius 2.0
+    pdie 2.0
+    sdie 78.54
+    srfm smol
+    chgm spl0
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# CALCULATE POTENTIAL FOR COMPLEX
+elec name complex
+    mg-para
+    ofrac 0.1
+    pdime 2 2 2
+    dime  97  97  97
+    fglen 112 91 116
+    cglen 156 121 162
+    cgcent mol 3
+    fgcent mol 3
+    mol 3
+    npbe
+    bcfl sdh
+    ion charge 1 conc 0.050 radius 2.0
+    ion charge -1 conc 0.050 radius 2.0 
+    pdie 2.0
+    sdie 78.54
+    srfm smol
+    chgm spl0
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+    write pot dx pot
+end
+
+# COMBINE TO GIVE BINDING ENERGY
+print elecEnergy complex - mol1 - mol2 end
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/actin-dimer/mesh.m

@@ -0,0 +1,43 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Dimension:     3
+% Domain:        Unit cube divided into six tetrahedra.
+% Boundary:      Four dirichlet bndry nodes (one cube face)
+%
+% rcsid="$Id$"
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+mcsf_begin=1;
+
+      dim=3;         % intrinsic manifold dimension
+    dimii=3;         % imbedding manifold dimension
+ vertices=8;         % number of vertices
+simplices=6;         % number of simplices
+
+vert=[
+%-------- ---- ----------------- ----------------- -----------------
+% Vert-ID Chrt X-Coordinate      Y-Coordinate      Z-Coordinate
+%-------- ---- ----------------- ----------------- -----------------
+0         0    -2.0000000000e+02 -2.0000000000e+02 -2.0000000000e+02
+1         0     2.0000000000e+02 -2.0000000000e+02 -2.0000000000e+02
+2         0    -2.0000000000e+02  2.0000000000e+02 -2.0000000000e+02
+3         0     2.0000000000e+02  2.0000000000e+02 -2.0000000000e+02
+4         0    -2.0000000000e+02 -2.0000000000e+02  2.0000000000e+02
+5         0     2.0000000000e+02 -2.0000000000e+02  2.0000000000e+02
+6         0    -2.0000000000e+02  2.0000000000e+02  2.0000000000e+02
+7         0     2.0000000000e+02  2.0000000000e+02  2.0000000000e+02
+];
+
+simp=[
+%-------- ---- ---- ------------------- ---------------------------------------
+% Simp-ID Grp  Mat  Face-Types          Vertex-Numbers
+%-------- ---- ---- ------------------- ---------------------------------------
+0         0    0    0    1    0    1    0 5 1 2
+1         0    0    0    1    1    0    0 5 2 4
+2         0    0    0    1    0    1    1 5 3 2
+3         0    0    0    1    0    1    3 5 7 2
+4         0    0    1    1    0    0    2 5 7 6
+5         0    0    1    1    0    0    2 5 6 4
+];
+
+mcsf_end=1;
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/alkanes/2-methylbutane.pdb

@@ -0,0 +1,19 @@
+COMPND      2-METHYLBUTANE
+AUTHOR      DAVE WOODCOCK  95 12 18
+ATOM      1  C  ALK      1       1.437  -1.308   0.657 0.000 1.908
+ATOM      2  C  ALK      1       0.739   0.054   0.519 0.000 1.908
+ATOM      3  C  ALK      1      -0.716  -0.170   0.083 0.000 1.908
+ATOM      4  C  ALK      1       1.514   0.916  -0.497 0.000 1.908
+ATOM      5  C  ALK      1      -1.514   1.145   0.036 0.000 1.908
+ATOM      6  H  ALK      1       0.900  -1.910   1.392 0.000 1.487
+ATOM      7  H  ALK      1       2.466  -1.154   0.989 0.000 1.487
+ATOM      8  H  ALK      1       1.428  -1.817  -0.308 0.000 1.487
+ATOM      9  H  ALK      1       0.764   0.554   1.489 0.000 1.487
+ATOM     10  H  ALK      1      -1.205  -0.834   0.798 0.000 1.487
+ATOM     11  H  ALK      1      -0.746  -0.628  -0.907 0.000 1.487
+ATOM     12  H  ALK      1       1.440   0.471  -1.489 0.000 1.487
+ATOM     13  H  ALK      1       2.567   0.936  -0.206 0.000 1.487
+ATOM     14  H  ALK      1       1.064   1.910  -0.530 0.000 1.487
+ATOM     15  H  ALK      1      -1.101   1.785  -0.745 0.000 1.487
+ATOM     16  H  ALK      1      -1.427   1.663   0.990 0.000 1.487
+ATOM     17  H  ALK      1      -2.567   0.904  -0.130 0.000 1.487

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/alkanes/README.md

@@ -0,0 +1,182 @@
+The example input files in this directory calculate nonpolar solvation energies for alkanes based on the protocol described in Wagoner JA, Baker NA. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci USA, 103, 8331-8336, 2006. [(http://dx.doi.org/10.1073/pnas.0600118103)](http://dx.doi.org/10.1073/pnas.0600118103).
+
+This example was contributed by Nathan Baker and Jason Wagoner.
+
+
+APBS Version|Alkane|SASA (Å<sup>2</sup>)|SASA energy (kJ/mol)|SAV (Å<sup>3</sup>)|SAV energy (kJ/mol)|WCA energy (kJ/mol)|Total nonpolar solvation energy (kJ/mol)
+---|---|---|---|---|---|---|---
+**3.0**|2-methylbutane|214.202|1.82072|253.665|60.7274|-48.1507|1.439739455792E+01
+||butane|193.855|1.64777|217.863|52.1564|-41.7207|1.208346456826E+01
+||cyclohexane|221.799|1.88529|267.435|64.0239|-52.3691|1.354016672221E+01
+||cyclopentane|193.638|1.64593|217.998|52.1887|-44.471|9.363673200142E+00
+||ethane|139.427|1.18513|140.346|33.5988|-25.3612|9.422717598546E+00
+||hexane|250.291|2.12748|298.053|71.3539|-57.0807|1.640068943201E+01
+||isobutane|192.744|1.63832|218.943|52.415|-40.8218|1.323144287435E+01
+||methane|105.42|0.896066|95.985|22.9788|-15.9805|7.894367190329E+00
+||neopentane|210.755|1.79141|251.127|60.1198|-47.4149|1.449633815052E+01
+||pentane|222.524|1.89145|258.93|61.9878|-49.4003|1.447900211546E+01
+||propane|170.391|1.44832|183.573|43.9474|-33.4721|1.192358496286E+01
+
+
+APBS Version|Alkane|SASA (Å<sup>2</sup>)|SASA energy (kJ/mol)|SAV (Å<sup>3</sup>)|SAV energy (kJ/mol)|WCA energy (kJ/mol)|Total nonpolar solvation energy (kJ/mol)
+---|---|---|---|---|---|---|---
+**1.5**|2-methylbutane|214.202|1.82072|253.665|60.7274|-48.1507|1.439739455792E+01
+||butane|193.855|1.64777|217.863|52.1564|-41.7207|1.208346456826E+01
+||cyclohexane|221.799|1.88529|267.435|64.0239|-52.3691|1.354016672221E+01
+||cyclopentane|193.638|1.64593|217.998|52.1887|-44.471|9.363673200142E+00
+||ethane|139.427|1.18513|140.346|33.5988|-25.3612|9.422717598546E+00
+||hexane|250.291|2.12748|298.053|71.3539|-57.0807|1.640068943201E+01
+||isobutane|192.744|1.63832|218.943|52.415|-40.8218|1.323144287435E+01
+||methane|105.42|0.896066|95.985|22.9788|-15.9805|7.894367190329E+00
+||neopentane|210.755|1.79141|251.127|60.1198|-47.4149|1.449633815052E+01
+||pentane|222.524|1.89145|258.93|61.9878|-49.4003|1.447900211546E+01
+||propane|170.391|1.44832|183.573|43.9474|-33.4721|1.192358496286E+01
+
+
+APBS Version|Alkane|SASA (Å<sup>2</sup>)|SASA energy (kJ/mol)|SAV (Å<sup>3</sup>)|SAV energy (kJ/mol)|WCA energy (kJ/mol)|Total nonpolar solvation energy (kJ/mol)
+---|---|---|---|---|---|---|---
+**1.4.2**|2-methylbutane|214.202|1.82072|253.665|60.7274|-48.1507|1.439740000000e+01
+||butane|193.855|1.64777|217.863|52.1564|-41.7207|1.208350000000e+01
+||cyclohexane|221.799|1.88529|267.435|64.0239|-52.3691|1.354020000000e+01
+||cyclopentane|193.638|1.64593|217.998|52.1887|-44.471|9.363670000000e+00
+||ethane|139.427|1.18513|140.346|33.5988|-25.3612|9.422720000000e+00
+||hexane|250.291|2.12748|298.053|71.3539|-57.0807|1.640070000000e+01
+||isobutane|192.744|1.63832|218.943|52.415|-40.8218|1.323140000000e+01
+||methane|105.42|0.896066|95.985|22.9788|-15.9805|7.894370000000e+00
+||neopentane|210.755|1.79141|251.127|60.1198|-47.4149|1.449630000000e+01
+||pentane|222.524|1.89145|258.93|61.9878|-49.4003|1.447900000000e+01
+||propane|170.391|1.44832|183.573|43.9474|-33.4721|1.192360000000e+01
+
+
+APBS Version|Alkane|SASA (Å<sup>2</sup>)|SASA energy (kJ/mol)|SAV (Å<sup>3</sup>)|SAV energy (kJ/mol)|WCA energy (kJ/mol)|Total nonpolar solvation energy (kJ/mol)
+---|---|---|---|---|---|---|---
+**1.4.1-binary**|2-methylbutane|214.202|1.82072|253.665|60.7274|-48.1507|1.439739455792E+01
+||butane|193.855|1.64777|217.863|52.1564|-41.7207|1.208346456826E+01
+||cyclohexane|221.799|1.88529|267.435|64.0239|-52.3691|1.354016672221E+01
+||cyclopentane|193.638|1.64593|217.998|52.1887|-44.471|9.363673200142E+00
+||ethane|139.427|1.18513|140.346|33.5988|-25.3612|9.422717598546E+00
+||hexane|250.291|2.12748|298.053|71.3539|-57.0807|1.640068943201E+01
+||isobutane|192.744|1.63832|218.943|52.415|-40.8218|1.323144287435E+01
+||methane|105.42|0.896066|95.985|22.9788|-15.9805|7.894367190329E+00
+||neopentane|210.755|1.79141|251.127|60.1198|-47.4149|1.449633815052E+01
+||pentane|222.524|1.89145|258.93|61.9878|-49.4003|1.447900211546E+01
+||propane|170.391|1.44832|183.573|43.9474|-33.4721|1.192358496286E+01
+
+
+APBS Version|Alkane|SASA (Å<sup>2</sup>)|SASA energy (kJ/mol)|SAV (Å<sup>3</sup>)|SAV energy (kJ/mol)|WCA energy (kJ/mol)|Total nonpolar solvation energy (kJ/mol)
+---|---|---|---|---|---|---|---
+**1.4**|2-methylbutane|214.202|1.82072|253.665|60.7274|-48.1507|1.439739455792E+01
+||butane|193.855|1.64777|217.863|52.1564|-41.7207|1.208346456826E+01
+||cyclohexane|221.799|1.88529|267.435|64.0239|-52.3691|1.354016672221E+01
+||cyclopentane|193.638|1.64593|217.998|52.1887|-44.471|9.363673200142E+00
+||ethane|139.427|1.18513|140.346|33.5988|-25.3612|9.422717598546E+00
+||hexane|250.291|2.12748|298.053|71.3539|-57.0807|1.640068943201E+01
+||isobutane|192.744|1.63832|218.943|52.415|-40.8218|1.323144287435E+01
+||methane|105.42|0.896066|95.985|22.9788|-15.9805|7.894367190329E+00
+||neopentane|210.755|1.79141|251.127|60.1198|-47.4149|1.449633815052E+01
+||pentane|222.524|1.89145|258.93|61.9878|-49.4003|1.447900211546E+01
+||propane|170.391|1.44832|183.573|43.9474|-33.4721|1.192358496286E+01
+
+APBS Version|Alkane|SASA (Å<sup>2</sup>)|SASA energy (kJ/mol)|SAV (Å<sup>3</sup>)|SAV energy (kJ/mol)|WCA energy (kJ/mol)|Total nonpolar solvation energy (kJ/mol)
+---|---|---|---|---|---|---|---
+**1.3**|2-methylbutane|214.202|1.82072|253.906|60.7852|-48.3035|1.439739455792E+01
+||butane|193.855|1.64777|218.119|52.2176|-41.6443|1.208346456826E+01
+||cyclohexane|221.799|1.88529|267.165|63.9593|-52.4787|1.354016672221E+01
+||cyclopentane|193.638|1.64593|218.412|52.2877|-44.3607|9.363673200142E+00
+||ethane|139.427|1.18513|140.692|33.6818|-25.4382|9.422717598546E+00
+||hexane|250.291|2.12748|297.703|71.2701|-57.1544|1.640068943201E+01
+||isobutane|192.744|1.63832|219.153|52.4652|-40.8617|1.323144287435E+01
+||methane|105.42|0.896066|95.4242|22.8446|-15.9414|7.894367190329E+00
+||neopentane|210.755|1.79141|251.314|60.1647|-47.4807|1.449633815052E+01
+||pentane|222.524|259.149|1.89145|62.0403|-49.456|1.447900211546E+01
+||propane|170.391|182.703|1.44832|43.739|-33.4629|1.192358496286E+01
+
+APBS Version|Alkane|SASA (Å<sup>2</sup>)|SASA energy (kJ/mol)|SAV (Å<sup>3</sup>)|SAV energy (kJ/mol)|WCA energy (kJ/mol)|Total nonpolar solvation energy (kJ/mol)
+---|---|---|---|---|---|---|---
+1.2.1|2-methylbutane|214.202|1.82072|253.906|60.7852|-48.3035|1.439739455792E+01
+||butane|193.855|1.64777|218.119|52.2176|-41.6443|1.208346456826E+01
+||cyclohexane|221.799|1.88529|267.165|63.9593|-52.4787|1.354016672221E+01
+||cyclopentane|193.638|1.64593|218.412|52.2877|-44.3607|9.363673200142E+00
+||ethane|139.427|1.18513|140.692|33.6818|-25.4382|9.422717598546E+00
+||hexane|250.291|2.12748|297.703|71.2701|-57.1544|1.640068943201E+01
+||isobutane|192.744|1.63832|219.153|52.4652|-40.8617|1.323144287435E+01
+||methane|105.42|0.896066|95.4242|22.8446|-15.9414|7.894367190329E+00
+||neopentane|210.755|1.79141|251.314|60.1647|-47.4807|1.449633815052E+01
+||pentane|222.524|259.149|1.89145|62.0403|-49.456|1.447900211546E+01
+||propane|170.391|182.703|1.44832|43.739|-33.4629|1.192358496286E+01
+
+APBS Version|Alkane|SASA (Å<sup>2</sup>)|SASA energy (kJ/mol)|SAV (Å<sup>3</sup>)|SAV energy (kJ/mol)|WCA energy (kJ/mol)|Total nonpolar solvation energy (kJ/mol)
+---|---|---|---|---|---|---|---
+1.2|2-methylbutane|214.202|1.82072|253.906|60.7852|-48.3035|1.439739455792E+01
+||butane|193.855|1.64777|218.119|52.2176|-41.6443|1.208346456826E+01
+||cyclohexane|221.799|1.88529|267.165|63.9593|-52.4787|1.354016672221E+01
+||cyclopentane|193.638|1.64593|218.412|52.2877|-44.3607|9.363673200142E+00
+||ethane|139.427|1.18513|140.692|33.6818|-25.4382|9.422717598546E+00
+||hexane|250.291|2.12748|297.703|71.2701|-57.1544|1.640068943201E+01
+||isobutane|192.744|1.63832|219.153|52.4652|-40.8617|1.323144287435E+01
+||methane|105.42|0.896066|95.4242|22.8446|-15.9414|7.894367190329E+00
+||neopentane|210.755|1.79141|251.314|60.1647|-47.4807|1.449633815052E+01
+||pentane|222.524|259.149|1.89145|62.0403|-49.456|1.447900211546E+01
+||propane|170.391|182.703|1.44832|43.739|-33.4629|1.192358496286E+01
+
+APBS Version|Alkane|SASA (Å<sup>2</sup>)|SASA energy (kJ/mol)|SAV (Å<sup>3</sup>)|SAV energy (kJ/mol)|WCA energy (kJ/mol)|Total nonpolar solvation energy (kJ/mol)
+---|---|---|---|---|---|---|---
+1.1.0|2-methylbutane|214.202|1.82072|253.906|60.7852|-48.3035|1.439739455792E+01
+||butane|193.855|1.64777|218.119|52.2176|-41.6443|1.208346456826E+01
+||cyclohexane|221.799|1.88529|267.165|63.9593|-52.4787|1.354016672221E+01
+||cyclopentane|193.638|1.64593|218.412|52.2877|-44.3607|9.363673200142E+00
+||ethane|139.427|1.18513|140.692|33.6818|-25.4382|9.422717598546E+00
+||hexane|250.291|2.12748|297.703|71.2701|-57.1544|1.640068943201E+01
+||isobutane|192.744|1.63832|219.153|52.4652|-40.8617|1.323144287435E+01
+||methane|105.42|0.896066|95.4242|22.8446|-15.9414|7.894367190329E+00
+||neopentane|210.755|1.79141|251.314|60.1647|-47.4807|1.449633815052E+01
+||pentane|222.524|259.149|1.89145|62.0403|-49.456|1.447900211546E+01
+||propane|170.391|182.703|1.44832|43.739|-33.4629|1.192358496286E+01
+
+APBS Version|Alkane|SASA (Å<sup>2</sup>)|SASA energy (kJ/mol)|SAV (Å<sup>3</sup>)|SAV energy (kJ/mol)|WCA energy (kJ/mol)|Total nonpolar solvation energy (kJ/mol)
+---|---|---|---|---|---|---|---
+1.0.0|2-methylbutane|214.202|1.82072|253.906|60.7852|-48.3035|1.439739455792E+01
+||butane|193.855|1.64777|218.119|52.2176|-41.6443|1.208346456826E+01
+||cyclohexane|221.799|1.88529|267.165|63.9593|-52.4787|1.354016672221E+01
+||cyclopentane|193.638|1.64593|218.412|52.2877|-44.3607|9.363673200142E+00
+||ethane|139.427|1.18513|140.692|33.6818|-25.4382|9.422717598546E+00
+||hexane|250.291|2.12748|297.703|71.2701|-57.1544|1.640068943201E+01
+||isobutane|192.744|1.63832|219.153|52.4652|-40.8617|1.323144287435E+01
+||methane|105.42|0.896066|95.4242|22.8446|-15.9414|7.894367190329E+00
+||neopentane|210.755|1.79141|251.314|60.1647|-47.4807|1.449633815052E+01
+||pentane|222.524|259.149|1.89145|62.0403|-49.456|1.447900211546E+01
+||propane|170.391|182.703|1.44832|43.739|-33.4629|1.192358496286E+01
+
+APBS Version|Alkane|SASA (Å<sup>2</sup>)|SASA energy (kJ/mol)|SAV (Å<sup>3</sup>)|SAV energy (kJ/mol)|WCA energy (kJ/mol)|Total nonpolar solvation energy (kJ/mol)
+---|---|---|---|---|---|---|---
+0.5.1<sup>[1](#1)</sup>|2-methylbutane|214.202|1.82072|253.906|60.7852|-48.3035|1.439739455792E+01
+||butane|193.855|1.64777|218.119|52.2176|-41.6443|1.208346456826E+01
+||cyclohexane|221.799|1.88529|267.165|63.9593|-52.4787|1.354016672221E+01
+||cyclopentane|193.638|1.64593|218.412|52.2877|-44.3607|9.363673200142E+00
+||ethane|139.427|1.18513|140.692|33.6818|-25.4382|9.422717598546E+00
+||hexane|250.291|2.12748|297.703|71.2701|-57.1544|1.640068943201E+01
+||isobutane|192.744|1.63832|219.153|52.4652|-40.8617|1.323144287435E+01
+||methane|105.42|0.896066|95.4242|22.8446|-15.9414|7.894367190329E+00
+||neopentane|210.755|1.79141|251.314|60.1647|-47.4807|1.449633815052E+01
+||pentane|222.524|259.149|1.89145|62.0403|-49.456|1.447900211546E+01
+||propane|170.391|182.703|1.44832|43.739|-33.4629|1.192358496286E+01
+
+APBS Version|Alkane|SASA (Å<sup>2</sup>)|SASA energy (kJ/mol)|SAV (Å<sup>3</sup>)|SAV energy (kJ/mol)|WCA energy (kJ/mol)|Total nonpolar solvation energy (kJ/mol)
+---|---|---|---|---|---|---|---
+0.5.0|2-methylbutane|214.202|1.82072|253.906|60.7852|-48.3035|1.430239579640E+01
+||butane|193.855|1.64777|218.119|52.2176|-41.6443|1.222110127537E+01
+||cyclohexane|221.799|1.88529|267.165|63.9593|-52.4787|1.336586748209E+01
+||cyclopentane|193.638|1.64593|218.412|52.2877|-44.3607|9.572911268235E+00
+||ethane|139.427|1.18513|140.692|33.6818|-25.4382|9.428701470984E+00
+||hexane|250.291|2.12748|297.703|71.2701|-57.1544|1.624316652259E+01
+||isobutane|192.744|1.63832|219.153|52.4652|-40.8617|1.324178842307E+01
+||methane|105.42|0.896066|95.4242|22.8446|-15.9414|7.799212389992E+00
+||neopentane|210.755|1.79141|251.314|60.1647|-47.4807|1.447540747648E+01
+||pentane|222.524|259.149|1.89145|62.0403|-49.456|1.447574303821E+01
+||propane|170.391|182.703|1.44832|43.739|-33.4629|1.172438897305E+01
+
+<a name=1></a><sup>1</sup> The discrepancy in values between versions 0.5.1 and 0.5.0 is most likely due to the following factor(s):
+
+-   Removal of the dime keyword and implementation of variable grid lengths
+
+Please see the ChangeLog or the [APBS website](http://www.poissonboltzmann.org/) for more information.

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/alkanes/alkanes.in

@@ -0,0 +1,205 @@
+
+read 
+	mol pdb 2-methylbutane.pdb
+	mol pdb butane.pdb
+	mol pdb cyclohexane.pdb
+	mol pdb cyclopentane.pdb
+	mol pdb ethane.pdb
+	mol pdb hexane.pdb
+	mol pdb isobutane.pdb
+	mol pdb methane.pdb
+	mol pdb neopentane.pdb
+	mol pdb pentane.pdb
+	mol pdb propane.pdb
+	parm flat parm.dat
+end
+
+APOLAR name solvated-2-methylbutane
+	grid 0.3 0.3 0.3
+	mol 1
+	srfm sacc
+	swin 0.3
+	srad 0.65
+	press 0.2394
+	gamma 0.0085
+	bconc 0.033428
+	sdens 100.0
+	dpos 0.2
+	temp 298.15
+	calcenergy total
+	calcforce no
+END
+
+APOLAR name solvated-butane
+	grid 0.3 0.3 0.3
+	mol 2
+	srfm sacc
+	swin 0.3
+	srad 0.65
+	press 0.2394
+	gamma 0.0085
+	bconc 0.033428
+	sdens 100.0
+	dpos 0.2
+	temp 298.15
+	calcenergy total
+	calcforce no
+END
+
+APOLAR name solvated-cyclohexane
+	grid 0.3 0.3 0.3
+	mol 3
+	srfm sacc
+	swin 0.3
+	srad 0.65
+	press 0.2394
+	gamma 0.0085
+	bconc 0.033428
+	sdens 100.0
+	dpos 0.2
+	temp 298.15
+	calcenergy total
+	calcforce no
+END
+
+APOLAR name solvated-cyclopentane
+	grid 0.3 0.3 0.3
+	mol 4
+	srfm sacc
+	swin 0.3
+	srad 0.65
+	press 0.2394
+	gamma 0.0085
+	bconc 0.033428
+	sdens 100.0
+	dpos 0.2
+	temp 298.15
+	calcenergy total
+	calcforce no
+END
+
+APOLAR name solvated-ethane
+	grid 0.3 0.3 0.3
+	mol 5
+	srfm sacc
+	swin 0.3
+	srad 0.65
+	press 0.2394
+	gamma 0.0085
+	bconc 0.033428
+	sdens 100.0
+	dpos 0.2
+	temp 298.15
+	calcenergy total
+	calcforce no
+END
+
+APOLAR name solvated-hexane
+	grid 0.3 0.3 0.3
+	mol 6
+	srfm sacc
+	swin 0.3
+	srad 0.65
+	press 0.2394
+	gamma 0.0085
+	bconc 0.033428
+	sdens 100.0
+	dpos 0.2
+	temp 298.15
+	calcenergy total
+	calcforce no
+END
+
+APOLAR name solvated-isobutane
+	grid 0.3 0.3 0.3
+	mol 7
+	srfm sacc
+	swin 0.3
+	srad 0.65
+	press 0.2394
+	gamma 0.0085
+	bconc 0.033428
+	sdens 100.0
+	dpos 0.2
+	temp 298.15
+	calcenergy total
+	calcforce no
+END
+
+APOLAR name solvated-methane
+	grid 0.3 0.3 0.3
+	mol 8
+	srfm sacc
+	swin 0.3
+	srad 0.65
+	press 0.2394
+	gamma 0.0085
+	bconc 0.033428
+	sdens 100.0
+	dpos 0.2
+	temp 298.15
+	calcenergy total
+	calcforce no
+END
+
+APOLAR name solvated-neopentane
+	grid 0.3 0.3 0.3
+	mol 9
+	srfm sacc
+	swin 0.3
+	srad 0.65
+	press 0.2394
+	gamma 0.0085
+	bconc 0.033428
+	sdens 100.0
+	dpos 0.2
+	temp 298.15
+	calcenergy total
+	calcforce no
+END
+
+APOLAR name solvated-pentane
+	grid 0.3 0.3 0.3
+	mol 10
+	srfm sacc
+	swin 0.3
+	srad 0.65
+	press 0.2394
+	gamma 0.0085
+	bconc 0.033428
+	sdens 100.0
+	dpos 0.2
+	temp 298.15
+	calcenergy total
+	calcforce no
+END
+
+APOLAR name solvated-propane
+	grid 0.3 0.3 0.3
+	mol 11
+	srfm sacc
+	swin 0.3
+	srad 0.65
+	press 0.2394
+	gamma 0.0085
+	bconc 0.033428
+	sdens 100.0
+	dpos 0.2
+	temp 298.15
+	calcenergy total
+	calcforce no
+END
+
+print apolEnergy solvated-2-methylbutane end
+print apolEnergy solvated-butane end
+print apolEnergy solvated-cyclohexane end
+print apolEnergy solvated-cyclopentane end
+print apolEnergy solvated-ethane end
+print apolEnergy solvated-hexane end
+print apolEnergy solvated-isobutane end
+print apolEnergy solvated-methane end
+print apolEnergy solvated-neopentane end
+print apolEnergy solvated-pentane end
+print apolEnergy solvated-propane end
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/alkanes/alkanes.out

@@ -0,0 +1,849 @@
+
+
+----------------------------------------------------------------------
+    APBS -- Adaptive Poisson-Boltzmann Solver
+    Version APBS 3.4.1
+    
+    Nathan A. Baker (nathan.baker@pnnl.gov)
+    Pacific Northwest National Laboratory
+    
+    Additional contributing authors listed in the code documentation.
+    
+    Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific
+    Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
+    Northwest Division for the U.S. Department of Energy.
+    
+    Portions Copyright (c) 2002-2010, Washington University in St. Louis.
+    Portions Copyright (c) 2002-2020, Nathan A. Baker.
+    Portions Copyright (c) 1999-2002, The Regents of the University of California.
+    Portions Copyright (c) 1995, Michael Holst.
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+    
+    * Redistributions of source code must retain the above copyright notice, this
+      list of conditions and the following disclaimer.
+    
+    * Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+    
+    * Neither the name of the developer nor the names of its contributors may be
+      used to endorse or promote products derived from this software without
+      specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+    ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+    ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+    (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+    LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+    ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+----------------------------------------------------------------------
+    APBS uses FETK (the Finite Element ToolKit) to solve the
+    Poisson-Boltzmann equation numerically.  FETK is a portable collection
+    of finite element modeling class libraries developed by the Michael Holst
+    research group and written in an object-oriented form of C.  FEtk is
+    designed to solve general coupled systems of nonlinear partial differential
+    equations using adaptive finite element methods, inexact Newton methods,
+    and algebraic multilevel methods.  More information about FEtk may be found
+    at <http://www.FEtk.ORG>.
+----------------------------------------------------------------------
+    APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
+    Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
+    which has been modified by Patrice Koehl
+    <http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
+    memory usage when solving the Poisson-Boltzmann equation.
+----------------------------------------------------------------------
+    Please cite your use of APBS as:
+
+    Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
+    nanosystems: application to microtubules and the ribosome. Proc.
+    Natl. Acad. Sci. USA 98, 10037-10041 2001.
+    
+
+This executable compiled on Apr 29 2022 at 19:42:46
+
+Parsing input file alkanes.in...
+rank 0 size 1...
+Parsed input file.
+Reading parameter data from parm.dat.
+Got paths for 11 molecules
+Reading PDB-format atom data from 2-methylbutane.pdb.
+  17 atoms
+  Centered at (0.000e+00, 0.000e+00, 0.000e+00)
+  Net charge 4.33e+00 e
+Reading PDB-format atom data from butane.pdb.
+  14 atoms
+  Centered at (3.917e+00, 7.025e-01, -8.575e+00)
+  Net charge 3.51e+00 e
+Reading PDB-format atom data from cyclohexane.pdb.
+  18 atoms
+  Centered at (1.123e+00, 5.880e-01, 7.680e-01)
+  Net charge 4.93e+00 e
+Reading PDB-format atom data from cyclopentane.pdb.
+  13 atoms
+  Centered at (1.320e+00, 5.255e-01, 1.289e+00)
+  Net charge 3.88e+00 e
+Reading PDB-format atom data from ethane.pdb.
+  8 atoms
+  Centered at (2.210e-01, -2.100e-02, 7.650e-01)
+  Net charge 1.87e+00 e
+Reading PDB-format atom data from hexane.pdb.
+  20 atoms
+  Centered at (4.951e+00, -9.500e-03, -8.406e+00)
+  Net charge 5.16e+00 e
+Reading PDB-format atom data from isobutane.pdb.
+  14 atoms
+  Centered at (1.859e+01, 1.864e+01, 1.921e+01)
+  Net charge 3.51e+00 e
+Reading PDB-format atom data from methane.pdb.
+  5 atoms
+  Centered at (1.803e+01, 1.779e+01, 1.782e+01)
+  Net charge 1.05e+00 e
+Reading PDB-format atom data from neopentane.pdb.
+  17 atoms
+  Centered at (1.867e+01, 1.894e+01, 1.920e+01)
+  Net charge 4.33e+00 e
+Reading PDB-format atom data from pentane.pdb.
+  17 atoms
+  Centered at (4.460e+00, 1.615e-01, -8.566e+00)
+  Net charge 4.33e+00 e
+Reading PDB-format atom data from propane.pdb.
+  11 atoms
+  Centered at (1.836e+01, 1.896e+01, 1.861e+01)
+  Net charge 2.69e+00 e
+Preparing to run 11 PBE calculations.
+----------------------------------------
+CALCULATION #1 (solvated-2-methylbutane): APOLAR
+
+Solvent Accessible Surface Area (SASA) for each atom:
+  SASA for atom 0: 3.815624614267E+00
+  SASA for atom 1: 0.000000000000E+00
+  SASA for atom 2: 6.122920124655E-01
+  SASA for atom 3: 3.957497153740E+00
+  SASA for atom 4: 4.308445014544E+00
+  SASA for atom 5: 1.843264951960E+01
+  SASA for atom 6: 1.837011296483E+01
+  SASA for atom 7: 1.666599184724E+01
+  SASA for atom 8: 1.480031796315E+01
+  SASA for atom 9: 1.603020354037E+01
+  SASA for atom 10: 1.473778140838E+01
+  SASA for atom 11: 1.611879699297E+01
+  SASA for atom 12: 1.810954398660E+01
+  SASA for atom 13: 1.420100931324E+01
+  SASA for atom 14: 1.437298483886E+01
+  SASA for atom 15: 1.814081226399E+01
+  SASA for atom 16: 2.152820898091E+01
+
+Total solvent accessible surface area: 214.202 A^2
+
+Surface tension*area energies (gamma * SASA) for each atom:
+  Surface tension*area energy for atom 0: 3.243280922127E-02
+  Surface tension*area energy for atom 1: 0.000000000000E+00
+  Surface tension*area energy for atom 2: 5.204482105957E-03
+  Surface tension*area energy for atom 3: 3.363872580679E-02
+  Surface tension*area energy for atom 4: 3.662178262362E-02
+  Surface tension*area energy for atom 5: 1.566775209166E-01
+  Surface tension*area energy for atom 6: 1.561459602010E-01
+  Surface tension*area energy for atom 7: 1.416609307015E-01
+  Surface tension*area energy for atom 8: 1.258027026868E-01
+  Surface tension*area energy for atom 9: 1.362567300932E-01
+  Surface tension*area energy for atom 10: 1.252711419712E-01
+  Surface tension*area energy for atom 11: 1.370097744402E-01
+  Surface tension*area energy for atom 12: 1.539311238861E-01
+  Surface tension*area energy for atom 13: 1.207085791625E-01
+  Surface tension*area energy for atom 14: 1.221703711303E-01
+  Surface tension*area energy for atom 15: 1.541969042439E-01
+  Surface tension*area energy for atom 16: 1.829897763377E-01
+
+Total surface tension energy: 1.82072 kJ/mol
+
+Total solvent accessible volume: 253.665 A^3
+
+Total pressure*volume energy: 60.7274 kJ/mol
+
+WCA dispersion Energies for each atom:
+  WCA energy for atom 0: -6.271287875274E+00
+  WCA energy for atom 1: -5.600872869478E+00
+  WCA energy for atom 2: -5.773775123943E+00
+  WCA energy for atom 3: -6.072801488986E+00
+  WCA energy for atom 4: -6.378470721845E+00
+  WCA energy for atom 5: -1.573474558351E+00
+  WCA energy for atom 6: -1.582338715648E+00
+  WCA energy for atom 7: -1.504044838266E+00
+  WCA energy for atom 8: -1.351002262819E+00
+  WCA energy for atom 9: -1.437367175239E+00
+  WCA energy for atom 10: -1.384626257493E+00
+  WCA energy for atom 11: -1.468867560891E+00
+  WCA energy for atom 12: -1.557005662832E+00
+  WCA energy for atom 13: -1.473759654043E+00
+  WCA energy for atom 14: -1.502261431335E+00
+  WCA energy for atom 15: -1.550940901474E+00
+  WCA energy for atom 16: -1.667828659696E+00
+
+Total WCA energy: -48.1507 kJ/mol
+
+Total non-polar energy = 1.439739455792E+01 kJ/mol
+----------------------------------------
+CALCULATION #2 (solvated-butane): APOLAR
+
+Solvent Accessible Surface Area (SASA) for each atom:
+  SASA for atom 0: 4.405515699447E+00
+  SASA for atom 1: 8.213673337951E-01
+  SASA for atom 2: 8.064333822716E-01
+  SASA for atom 3: 4.375647796400E+00
+  SASA for atom 4: 1.855251124959E+01
+  SASA for atom 5: 2.147609518526E+01
+  SASA for atom 6: 1.852645435176E+01
+  SASA for atom 7: 1.660345529247E+01
+  SASA for atom 8: 1.658782115377E+01
+  SASA for atom 9: 1.658260977421E+01
+  SASA for atom 10: 1.658260977421E+01
+  SASA for atom 11: 2.145003828744E+01
+  SASA for atom 12: 1.852124297220E+01
+  SASA for atom 13: 1.856293400871E+01
+
+Total solvent accessible surface area: 193.855 A^2
+
+Surface tension*area energies (gamma * SASA) for each atom:
+  Surface tension*area energy for atom 0: 3.744688344530E-02
+  Surface tension*area energy for atom 1: 6.981622337259E-03
+  Surface tension*area energy for atom 2: 6.854683749309E-03
+  Surface tension*area energy for atom 3: 3.719300626940E-02
+  Surface tension*area energy for atom 4: 1.576963456215E-01
+  Surface tension*area energy for atom 5: 1.825468090747E-01
+  Surface tension*area energy for atom 6: 1.574748619900E-01
+  Surface tension*area energy for atom 7: 1.411293699860E-01
+  Surface tension*area energy for atom 8: 1.409964798071E-01
+  Surface tension*area energy for atom 9: 1.409521830808E-01
+  Surface tension*area energy for atom 10: 1.409521830808E-01
+  Surface tension*area energy for atom 11: 1.823253254433E-01
+  Surface tension*area energy for atom 12: 1.574305652637E-01
+  Surface tension*area energy for atom 13: 1.577849390741E-01
+
+Total surface tension energy: 1.64777 kJ/mol
+
+Total solvent accessible volume: 217.863 A^3
+
+Total pressure*volume energy: 52.1564 kJ/mol
+
+WCA dispersion Energies for each atom:
+  WCA energy for atom 0: -6.728858147814E+00
+  WCA energy for atom 1: -6.204037472587E+00
+  WCA energy for atom 2: -6.202937735018E+00
+  WCA energy for atom 3: -6.728762249931E+00
+  WCA energy for atom 4: -1.623549989062E+00
+  WCA energy for atom 5: -1.709092300778E+00
+  WCA energy for atom 6: -1.625196457114E+00
+  WCA energy for atom 7: -1.484289341167E+00
+  WCA energy for atom 8: -1.485410538626E+00
+  WCA energy for atom 9: -1.485593139015E+00
+  WCA energy for atom 10: -1.484878734279E+00
+  WCA energy for atom 11: -1.708585062695E+00
+  WCA energy for atom 12: -1.625094916482E+00
+  WCA energy for atom 13: -1.624416805392E+00
+
+Total WCA energy: -41.7207 kJ/mol
+
+Total non-polar energy = 1.208346456826E+01 kJ/mol
+----------------------------------------
+CALCULATION #3 (solvated-cyclohexane): APOLAR
+
+Solvent Accessible Surface Area (SASA) for each atom:
+  SASA for atom 0: 7.840324549863E-01
+  SASA for atom 1: 8.064333822716E-01
+  SASA for atom 2: 8.288343095569E-01
+  SASA for atom 3: 7.840324549863E-01
+  SASA for atom 4: 7.989664065098E-01
+  SASA for atom 5: 8.363012853187E-01
+  SASA for atom 6: 2.001169752764E+01
+  SASA for atom 7: 1.616048802948E+01
+  SASA for atom 8: 2.001169752764E+01
+  SASA for atom 9: 1.619175630687E+01
+  SASA for atom 10: 1.616048802948E+01
+  SASA for atom 11: 1.993352683418E+01
+  SASA for atom 12: 2.001169752764E+01
+  SASA for atom 13: 1.618133354774E+01
+  SASA for atom 14: 1.617091078861E+01
+  SASA for atom 15: 2.001690890721E+01
+  SASA for atom 16: 1.993873821374E+01
+  SASA for atom 17: 1.617091078861E+01
+
+Total solvent accessible surface area: 221.799 A^2
+
+Surface tension*area energies (gamma * SASA) for each atom:
+  Surface tension*area energy for atom 0: 6.664275867383E-03
+  Surface tension*area energy for atom 1: 6.854683749309E-03
+  Surface tension*area energy for atom 2: 7.045091631234E-03
+  Surface tension*area energy for atom 3: 6.664275867383E-03
+  Surface tension*area energy for atom 4: 6.791214455333E-03
+  Surface tension*area energy for atom 5: 7.108560925209E-03
+  Surface tension*area energy for atom 6: 1.700994289850E-01
+  Surface tension*area energy for atom 7: 1.373641482506E-01
+  Surface tension*area energy for atom 8: 1.700994289850E-01
+  Surface tension*area energy for atom 9: 1.376299286084E-01
+  Surface tension*area energy for atom 10: 1.373641482506E-01
+  Surface tension*area energy for atom 11: 1.694349780905E-01
+  Surface tension*area energy for atom 12: 1.700994289850E-01
+  Surface tension*area energy for atom 13: 1.375413351558E-01
+  Surface tension*area energy for atom 14: 1.374527417032E-01
+  Surface tension*area energy for atom 15: 1.701437257113E-01
+  Surface tension*area energy for atom 16: 1.694792748168E-01
+  Surface tension*area energy for atom 17: 1.374527417032E-01
+
+Total surface tension energy: 1.88529 kJ/mol
+
+Total solvent accessible volume: 267.435 A^3
+
+Total pressure*volume energy: 64.0239 kJ/mol
+
+WCA dispersion Energies for each atom:
+  WCA energy for atom 0: -5.793234697241E+00
+  WCA energy for atom 1: -5.784370526583E+00
+  WCA energy for atom 2: -5.791799130412E+00
+  WCA energy for atom 3: -5.788504399087E+00
+  WCA energy for atom 4: -5.797319672490E+00
+  WCA energy for atom 5: -5.787358035342E+00
+  WCA energy for atom 6: -1.523887929614E+00
+  WCA energy for atom 7: -1.413678912317E+00
+  WCA energy for atom 8: -1.521751604392E+00
+  WCA energy for atom 9: -1.414741802525E+00
+  WCA energy for atom 10: -1.413367854344E+00
+  WCA energy for atom 11: -1.523407238081E+00
+  WCA energy for atom 12: -1.523000623583E+00
+  WCA energy for atom 13: -1.413922068538E+00
+  WCA energy for atom 14: -1.416316744211E+00
+  WCA energy for atom 15: -1.524577474659E+00
+  WCA energy for atom 16: -1.523300410052E+00
+  WCA energy for atom 17: -1.414522566061E+00
+
+Total WCA energy: -52.3691 kJ/mol
+
+Total non-polar energy = 1.354016672221E+01 kJ/mol
+----------------------------------------
+CALCULATION #4 (solvated-cyclopentane): APOLAR
+
+Solvent Accessible Surface Area (SASA) for each atom:
+  SASA for atom 0: 9.490526193215E+00
+  SASA for atom 1: 9.512927120500E+00
+  SASA for atom 2: 2.299828534626E+00
+  SASA for atom 3: 1.919012770776E+00
+  SASA for atom 4: 2.307295510388E+00
+  SASA for atom 5: 2.325838699632E+01
+  SASA for atom 6: 2.325838699632E+01
+  SASA for atom 7: 2.045987617019E+01
+  SASA for atom 8: 2.067875411190E+01
+  SASA for atom 9: 2.028790064456E+01
+  SASA for atom 10: 1.897463299431E+01
+  SASA for atom 11: 2.048593306801E+01
+  SASA for atom 12: 2.070481100972E+01
+
+Total solvent accessible surface area: 193.638 A^2
+
+Surface tension*area energies (gamma * SASA) for each atom:
+  Surface tension*area energy for atom 0: 8.066947264233E-02
+  Surface tension*area energy for atom 1: 8.085988052425E-02
+  Surface tension*area energy for atom 2: 1.954854254432E-02
+  Surface tension*area energy for atom 3: 1.631160855160E-02
+  Surface tension*area energy for atom 4: 1.961201183830E-02
+  Surface tension*area energy for atom 5: 1.976962894687E-01
+  Surface tension*area energy for atom 6: 1.976962894687E-01
+  Surface tension*area energy for atom 7: 1.739089474466E-01
+  Surface tension*area energy for atom 8: 1.757694099511E-01
+  Surface tension*area energy for atom 9: 1.724471554788E-01
+  Surface tension*area energy for atom 10: 1.612843804516E-01
+  Surface tension*area energy for atom 11: 1.741304310781E-01
+  Surface tension*area energy for atom 12: 1.759908935826E-01
+
+Total surface tension energy: 1.64593 kJ/mol
+
+Total solvent accessible volume: 217.998 A^3
+
+Total pressure*volume energy: 52.1887 kJ/mol
+
+WCA dispersion Energies for each atom:
+  WCA energy for atom 0: -6.343496616804E+00
+  WCA energy for atom 1: -6.327869601807E+00
+  WCA energy for atom 2: -6.334858040579E+00
+  WCA energy for atom 3: -6.296075406417E+00
+  WCA energy for atom 4: -6.345600816761E+00
+  WCA energy for atom 5: -1.663697465126E+00
+  WCA energy for atom 6: -1.662444032853E+00
+  WCA energy for atom 7: -1.572325104493E+00
+  WCA energy for atom 8: -1.604626551065E+00
+  WCA energy for atom 9: -1.586431484963E+00
+  WCA energy for atom 10: -1.554291291374E+00
+  WCA energy for atom 11: -1.574315220751E+00
+  WCA energy for atom 12: -1.604941679892E+00
+
+Total WCA energy: -44.471 kJ/mol
+
+Total non-polar energy = 9.363673200142E+00 kJ/mol
+----------------------------------------
+CALCULATION #5 (solvated-ethane): APOLAR
+
+Solvent Accessible Surface Area (SASA) for each atom:
+  SASA for atom 0: 5.995981536705E+00
+  SASA for atom 1: 5.966113633657E+00
+  SASA for atom 2: 2.121552620704E+01
+  SASA for atom 3: 2.124158310486E+01
+  SASA for atom 4: 2.125200586399E+01
+  SASA for atom 5: 2.123116034573E+01
+  SASA for atom 6: 2.125200586399E+01
+  SASA for atom 7: 2.127285138225E+01
+
+Total solvent accessible surface area: 139.427 A^2
+
+Surface tension*area energies (gamma * SASA) for each atom:
+  Surface tension*area energy for atom 0: 5.096584306199E-02
+  Surface tension*area energy for atom 1: 5.071196588609E-02
+  Surface tension*area energy for atom 2: 1.803319727598E-01
+  Surface tension*area energy for atom 3: 1.805534563913E-01
+  Surface tension*area energy for atom 4: 1.806420498439E-01
+  Surface tension*area energy for atom 5: 1.804648629387E-01
+  Surface tension*area energy for atom 6: 1.806420498439E-01
+  Surface tension*area energy for atom 7: 1.808192367491E-01
+
+Total surface tension energy: 1.18513 kJ/mol
+
+Total solvent accessible volume: 140.346 A^3
+
+Total pressure*volume energy: 33.5988 kJ/mol
+
+WCA dispersion Energies for each atom:
+  WCA energy for atom 0: -7.360066353115E+00
+  WCA energy for atom 1: -7.355483516201E+00
+  WCA energy for atom 2: -1.776106201066E+00
+  WCA energy for atom 3: -1.773973940651E+00
+  WCA energy for atom 4: -1.775401936843E+00
+  WCA energy for atom 5: -1.773464835521E+00
+  WCA energy for atom 6: -1.774382856097E+00
+  WCA energy for atom 7: -1.772366599434E+00
+
+Total WCA energy: -25.3612 kJ/mol
+
+Total non-polar energy = 9.422717598546E+00 kJ/mol
+----------------------------------------
+CALCULATION #6 (solvated-hexane): APOLAR
+
+Solvent Accessible Surface Area (SASA) for each atom:
+  SASA for atom 0: 4.405515699447E+00
+  SASA for atom 1: 8.213673337951E-01
+  SASA for atom 2: 3.285469335181E-01
+  SASA for atom 3: 2.986790304710E-01
+  SASA for atom 4: 1.855251124959E+01
+  SASA for atom 5: 2.147609518526E+01
+  SASA for atom 6: 1.852645435176E+01
+  SASA for atom 7: 1.655655287639E+01
+  SASA for atom 8: 1.655134149682E+01
+  SASA for atom 9: 1.360170066332E+01
+  SASA for atom 10: 1.357043238593E+01
+  SASA for atom 11: 1.381536722546E+01
+  SASA for atom 12: 1.384142412329E+01
+  SASA for atom 13: 7.765654792245E-01
+  SASA for atom 14: 1.684839013200E+01
+  SASA for atom 15: 1.682233323417E+01
+  SASA for atom 16: 4.166572475070E+00
+  SASA for atom 17: 2.179398933870E+01
+  SASA for atom 18: 1.877660057086E+01
+  SASA for atom 19: 1.876096643216E+01
+
+Total solvent accessible surface area: 250.291 A^2
+
+Surface tension*area energies (gamma * SASA) for each atom:
+  Surface tension*area energy for atom 0: 3.744688344530E-02
+  Surface tension*area energy for atom 1: 6.981622337259E-03
+  Surface tension*area energy for atom 2: 2.792648934903E-03
+  Surface tension*area energy for atom 3: 2.538771759003E-03
+  Surface tension*area energy for atom 4: 1.576963456215E-01
+  Surface tension*area energy for atom 5: 1.825468090747E-01
+  Surface tension*area energy for atom 6: 1.574748619900E-01
+  Surface tension*area energy for atom 7: 1.407306994493E-01
+  Surface tension*area energy for atom 8: 1.406864027230E-01
+  Surface tension*area energy for atom 9: 1.156144556382E-01
+  Surface tension*area energy for atom 10: 1.153486752804E-01
+  Surface tension*area energy for atom 11: 1.174306214164E-01
+  Surface tension*area energy for atom 12: 1.176521050479E-01
+  Surface tension*area energy for atom 13: 6.600806573408E-03
+  Surface tension*area energy for atom 14: 1.432113161220E-01
+  Surface tension*area energy for atom 15: 1.429898324905E-01
+  Surface tension*area energy for atom 16: 3.541586603809E-02
+  Surface tension*area energy for atom 17: 1.852489093789E-01
+  Surface tension*area energy for atom 18: 1.596011048523E-01
+  Surface tension*area energy for atom 19: 1.594682146734E-01
+
+Total surface tension energy: 2.12748 kJ/mol
+
+Total solvent accessible volume: 298.053 A^3
+
+Total pressure*volume energy: 71.3539 kJ/mol
+
+WCA dispersion Energies for each atom:
+  WCA energy for atom 0: -6.635406071935E+00
+  WCA energy for atom 1: -5.957247427848E+00
+  WCA energy for atom 2: -5.524801144538E+00
+  WCA energy for atom 3: -5.522294168859E+00
+  WCA energy for atom 4: -1.605314409440E+00
+  WCA energy for atom 5: -1.701051761776E+00
+  WCA energy for atom 6: -1.606669162773E+00
+  WCA energy for atom 7: -1.442505934938E+00
+  WCA energy for atom 8: -1.443059002759E+00
+  WCA energy for atom 9: -1.328947132810E+00
+  WCA energy for atom 10: -1.328906972440E+00
+  WCA energy for atom 11: -1.331566344214E+00
+  WCA energy for atom 12: -1.328041776815E+00
+  WCA energy for atom 13: -5.937562025661E+00
+  WCA energy for atom 14: -1.442277774427E+00
+  WCA energy for atom 15: -1.442777091510E+00
+  WCA energy for atom 16: -6.602262542378E+00
+  WCA energy for atom 17: -1.698172146664E+00
+  WCA energy for atom 18: -1.600970858835E+00
+  WCA energy for atom 19: -1.600841970217E+00
+
+Total WCA energy: -57.0807 kJ/mol
+
+Total non-polar energy = 1.640068943201E+01 kJ/mol
+----------------------------------------
+CALCULATION #7 (solvated-isobutane): APOLAR
+
+Solvent Accessible Surface Area (SASA) for each atom:
+  SASA for atom 0: 3.464676753463E+00
+  SASA for atom 1: 1.984493338158E+01
+  SASA for atom 2: 1.778643845361E+01
+  SASA for atom 3: 1.671289426332E+01
+  SASA for atom 4: 0.000000000000E+00
+  SASA for atom 5: 3.531879535319E+00
+  SASA for atom 6: 1.673895116114E+01
+  SASA for atom 7: 1.793756846098E+01
+  SASA for atom 8: 1.973549441072E+01
+  SASA for atom 9: 1.710895911022E+01
+  SASA for atom 10: 4.599657069253E+00
+  SASA for atom 11: 1.937069784121E+01
+  SASA for atom 12: 1.654613011726E+01
+  SASA for atom 13: 1.936548646165E+01
+
+Total solvent accessible surface area: 192.744 A^2
+
+Surface tension*area energies (gamma * SASA) for each atom:
+  Surface tension*area energy for atom 0: 2.944975240444E-02
+  Surface tension*area energy for atom 1: 1.686819337434E-01
+  Surface tension*area energy for atom 2: 1.511847268556E-01
+  Surface tension*area energy for atom 3: 1.420596012382E-01
+  Surface tension*area energy for atom 4: 0.000000000000E+00
+  Surface tension*area energy for atom 5: 3.002097605021E-02
+  Surface tension*area energy for atom 6: 1.422810848697E-01
+  Surface tension*area energy for atom 7: 1.524693319183E-01
+  Surface tension*area energy for atom 8: 1.677517024912E-01
+  Surface tension*area energy for atom 9: 1.454261524369E-01
+  Surface tension*area energy for atom 10: 3.909708508865E-02
+  Surface tension*area energy for atom 11: 1.646509316503E-01
+  Surface tension*area energy for atom 12: 1.406421059967E-01
+  Surface tension*area energy for atom 13: 1.646066349240E-01
+
+Total surface tension energy: 1.63832 kJ/mol
+
+Total solvent accessible volume: 218.943 A^3
+
+Total pressure*volume energy: 52.415 kJ/mol
+
+WCA dispersion Energies for each atom:
+  WCA energy for atom 0: -6.381016335247E+00
+  WCA energy for atom 1: -1.612317964554E+00
+  WCA energy for atom 2: -1.588013719598E+00
+  WCA energy for atom 3: -1.532162371190E+00
+  WCA energy for atom 4: -5.987950445279E+00
+  WCA energy for atom 5: -6.393089030861E+00
+  WCA energy for atom 6: -1.533454887042E+00
+  WCA energy for atom 7: -1.587650918485E+00
+  WCA energy for atom 8: -1.614083521570E+00
+  WCA energy for atom 9: -1.442402031577E+00
+  WCA energy for atom 10: -6.408813541353E+00
+  WCA energy for atom 11: -1.605830214390E+00
+  WCA energy for atom 12: -1.529385873788E+00
+  WCA energy for atom 13: -1.605662490385E+00
+
+Total WCA energy: -40.8218 kJ/mol
+
+Total non-polar energy = 1.323144287435E+01 kJ/mol
+----------------------------------------
+CALCULATION #8 (solvated-methane): APOLAR
+
+Solvent Accessible Surface Area (SASA) for each atom:
+  SASA for atom 0: 1.231304303117E+01
+  SASA for atom 1: 2.323233009850E+01
+  SASA for atom 2: 2.345641941977E+01
+  SASA for atom 3: 2.377431357320E+01
+  SASA for atom 4: 2.264344420771E+01
+
+Total solvent accessible surface area: 105.42 A^2
+
+Surface tension*area energies (gamma * SASA) for each atom:
+  Surface tension*area energy for atom 0: 1.046608657649E-01
+  Surface tension*area energy for atom 1: 1.974748058372E-01
+  Surface tension*area energy for atom 2: 1.993795650680E-01
+  Surface tension*area energy for atom 3: 2.020816653722E-01
+  Surface tension*area energy for atom 4: 1.924692757655E-01
+
+Total surface tension energy: 0.896066 kJ/mol
+
+Total solvent accessible volume: 95.985 A^3
+
+Total pressure*volume energy: 22.9788 kJ/mol
+
+WCA dispersion Energies for each atom:
+  WCA energy for atom 0: -8.133807570805E+00
+  WCA energy for atom 1: -1.962181541765E+00
+  WCA energy for atom 2: -1.964078319162E+00
+  WCA energy for atom 3: -1.963015006647E+00
+  WCA energy for atom 4: -1.957425549100E+00
+
+Total WCA energy: -15.9805 kJ/mol
+
+Total non-polar energy = 7.894367190329E+00 kJ/mol
+----------------------------------------
+CALCULATION #9 (solvated-neopentane): APOLAR
+
+Solvent Accessible Surface Area (SASA) for each atom:
+  SASA for atom 0: 2.441701074100E+00
+  SASA for atom 1: 1.663993494942E+01
+  SASA for atom 2: 1.715586152630E+01
+  SASA for atom 3: 1.645753666466E+01
+  SASA for atom 4: 0.000000000000E+00
+  SASA for atom 5: 2.389432243768E+00
+  SASA for atom 6: 1.638457735076E+01
+  SASA for atom 7: 1.667641460637E+01
+  SASA for atom 8: 1.721839808108E+01
+  SASA for atom 9: 2.419300146815E+00
+  SASA for atom 10: 1.640021148945E+01
+  SASA for atom 11: 1.666599184724E+01
+  SASA for atom 12: 1.719234118325E+01
+  SASA for atom 13: 2.449168049862E+00
+  SASA for atom 14: 1.723403221977E+01
+  SASA for atom 15: 1.639500010989E+01
+  SASA for atom 16: 1.663472356985E+01
+
+Total solvent accessible surface area: 210.755 A^2
+
+Surface tension*area energies (gamma * SASA) for each atom:
+  Surface tension*area energy for atom 0: 2.075445912985E-02
+  Surface tension*area energy for atom 1: 1.414394470700E-01
+  Surface tension*area energy for atom 2: 1.458248229736E-01
+  Surface tension*area energy for atom 3: 1.398890616496E-01
+  Surface tension*area energy for atom 4: 0.000000000000E+00
+  Surface tension*area energy for atom 5: 2.031017407203E-02
+  Surface tension*area energy for atom 6: 1.392689074814E-01
+  Surface tension*area energy for atom 7: 1.417495241541E-01
+  Surface tension*area energy for atom 8: 1.463563836891E-01
+  Surface tension*area energy for atom 9: 2.056405124793E-02
+  Surface tension*area energy for atom 10: 1.394017976603E-01
+  Surface tension*area energy for atom 11: 1.416609307015E-01
+  Surface tension*area energy for atom 12: 1.461349000577E-01
+  Surface tension*area energy for atom 13: 2.081792842383E-02
+  Surface tension*area energy for atom 14: 1.464892738680E-01
+  Surface tension*area energy for atom 15: 1.393575009340E-01
+  Surface tension*area energy for atom 16: 1.413951503437E-01
+
+Total surface tension energy: 1.79141 kJ/mol
+
+Total solvent accessible volume: 251.127 A^3
+
+Total pressure*volume energy: 60.1198 kJ/mol
+
+WCA dispersion Energies for each atom:
+  WCA energy for atom 0: -6.011082520236E+00
+  WCA energy for atom 1: -1.497367782613E+00
+  WCA energy for atom 2: -1.498546483218E+00
+  WCA energy for atom 3: -1.492562171495E+00
+  WCA energy for atom 4: -5.447325863939E+00
+  WCA energy for atom 5: -6.004516149175E+00
+  WCA energy for atom 6: -1.492776531092E+00
+  WCA energy for atom 7: -1.496078170066E+00
+  WCA energy for atom 8: -1.501529655270E+00
+  WCA energy for atom 9: -5.996267554365E+00
+  WCA energy for atom 10: -1.492194267752E+00
+  WCA energy for atom 11: -1.496027211216E+00
+  WCA energy for atom 12: -1.500561393960E+00
+  WCA energy for atom 13: -6.000218612907E+00
+  WCA energy for atom 14: -1.500859921426E+00
+  WCA energy for atom 15: -1.492908499790E+00
+  WCA energy for atom 16: -1.494057174414E+00
+
+Total WCA energy: -47.4149 kJ/mol
+
+Total non-polar energy = 1.449633815052E+01 kJ/mol
+----------------------------------------
+CALCULATION #10 (solvated-pentane): APOLAR
+
+Solvent Accessible Surface Area (SASA) for each atom:
+  SASA for atom 0: 4.405515699447E+00
+  SASA for atom 1: 8.213673337951E-01
+  SASA for atom 2: 3.285469335181E-01
+  SASA for atom 3: 7.466975761774E-01
+  SASA for atom 4: 1.855251124959E+01
+  SASA for atom 5: 2.147609518526E+01
+  SASA for atom 6: 1.852645435176E+01
+  SASA for atom 7: 1.655655287639E+01
+  SASA for atom 8: 1.655134149682E+01
+  SASA for atom 9: 1.360170066332E+01
+  SASA for atom 10: 1.357043238593E+01
+  SASA for atom 11: 1.685881289113E+01
+  SASA for atom 12: 1.687444702982E+01
+  SASA for atom 13: 4.196440378117E+00
+  SASA for atom 14: 1.881308022781E+01
+  SASA for atom 15: 1.882350298694E+01
+  SASA for atom 16: 2.182004623652E+01
+
+Total solvent accessible surface area: 222.524 A^2
+
+Surface tension*area energies (gamma * SASA) for each atom:
+  Surface tension*area energy for atom 0: 3.744688344530E-02
+  Surface tension*area energy for atom 1: 6.981622337259E-03
+  Surface tension*area energy for atom 2: 2.792648934903E-03
+  Surface tension*area energy for atom 3: 6.346929397508E-03
+  Surface tension*area energy for atom 4: 1.576963456215E-01
+  Surface tension*area energy for atom 5: 1.825468090747E-01
+  Surface tension*area energy for atom 6: 1.574748619900E-01
+  Surface tension*area energy for atom 7: 1.407306994493E-01
+  Surface tension*area energy for atom 8: 1.406864027230E-01
+  Surface tension*area energy for atom 9: 1.156144556382E-01
+  Surface tension*area energy for atom 10: 1.153486752804E-01
+  Surface tension*area energy for atom 11: 1.432999095746E-01
+  Surface tension*area energy for atom 12: 1.434327997535E-01
+  Surface tension*area energy for atom 13: 3.566974321399E-02
+  Surface tension*area energy for atom 14: 1.599111819364E-01
+  Surface tension*area energy for atom 15: 1.599997753890E-01
+  Surface tension*area energy for atom 16: 1.854703930104E-01
+
+Total surface tension energy: 1.89145 kJ/mol
+
+Total solvent accessible volume: 258.93 A^3
+
+Total pressure*volume energy: 61.9878 kJ/mol
+
+WCA dispersion Energies for each atom:
+  WCA energy for atom 0: -6.655804319869E+00
+  WCA energy for atom 1: -6.027315962813E+00
+  WCA energy for atom 2: -5.696430965386E+00
+  WCA energy for atom 3: -6.016749084714E+00
+  WCA energy for atom 4: -1.608595384643E+00
+  WCA energy for atom 5: -1.703300955380E+00
+  WCA energy for atom 6: -1.609931495887E+00
+  WCA energy for atom 7: -1.457107525189E+00
+  WCA energy for atom 8: -1.457741620594E+00
+  WCA energy for atom 9: -1.354235498709E+00
+  WCA energy for atom 10: -1.354106470090E+00
+  WCA energy for atom 11: -1.456736412636E+00
+  WCA energy for atom 12: -1.455995435596E+00
+  WCA energy for atom 13: -6.633650611186E+00
+  WCA energy for atom 14: -1.605996088477E+00
+  WCA energy for atom 15: -1.606549890103E+00
+  WCA energy for atom 16: -1.700042300035E+00
+
+Total WCA energy: -49.4003 kJ/mol
+
+Total non-polar energy = 1.447900211546E+01 kJ/mol
+----------------------------------------
+CALCULATION #11 (solvated-propane): APOLAR
+
+Solvent Accessible Surface Area (SASA) for each atom:
+  SASA for atom 0: 3.173464698754E+00
+  SASA for atom 1: 1.931858404557E+01
+  SASA for atom 2: 2.014198201675E+01
+  SASA for atom 3: 2.149694070352E+01
+  SASA for atom 4: 1.904078819252E+00
+  SASA for atom 5: 2.067354273233E+01
+  SASA for atom 6: 1.937590922077E+01
+  SASA for atom 7: 3.098794941136E+00
+  SASA for atom 8: 1.942802301642E+01
+  SASA for atom 9: 1.973028303116E+01
+  SASA for atom 10: 2.204934693736E+01
+
+Total solvent accessible surface area: 170.391 A^2
+
+Surface tension*area energies (gamma * SASA) for each atom:
+  Surface tension*area energy for atom 0: 2.697444993941E-02
+  Surface tension*area energy for atom 1: 1.642079643873E-01
+  Surface tension*area energy for atom 2: 1.712068471424E-01
+  Surface tension*area energy for atom 3: 1.827239959799E-01
+  Surface tension*area energy for atom 4: 1.618466996365E-02
+  Surface tension*area energy for atom 5: 1.757251132248E-01
+  Surface tension*area energy for atom 6: 1.646952283766E-01
+  Surface tension*area energy for atom 7: 2.633975699966E-02
+  Surface tension*area energy for atom 8: 1.651381956396E-01
+  Surface tension*area energy for atom 9: 1.677074057649E-01
+  Surface tension*area energy for atom 10: 1.874194489675E-01
+
+Total surface tension energy: 1.44832 kJ/mol
+
+Total solvent accessible volume: 183.573 A^3
+
+Total pressure*volume energy: 43.9474 kJ/mol
+
+WCA dispersion Energies for each atom:
+  WCA energy for atom 0: -6.818670105515E+00
+  WCA energy for atom 1: -1.641297645338E+00
+  WCA energy for atom 2: -1.649584120441E+00
+  WCA energy for atom 3: -1.711408141255E+00
+  WCA energy for atom 4: -6.624720142882E+00
+  WCA energy for atom 5: -1.610117050515E+00
+  WCA energy for atom 6: -1.596858009746E+00
+  WCA energy for atom 7: -6.816460624835E+00
+  WCA energy for atom 8: -1.642782751806E+00
+  WCA energy for atom 9: -1.645779566650E+00
+  WCA energy for atom 10: -1.714436154542E+00
+
+Total WCA energy: -33.4721 kJ/mol
+
+Total non-polar energy = 1.192358496286E+01 kJ/mol
+----------------------------------------
+PRINT STATEMENTS
+
+print APOL energy 1 (solvated-2-methylbutane) end
+  Global net APOL energy = 1.439739455792E+01 kJ/mol
+
+print APOL energy 2 (solvated-butane) end
+  Global net APOL energy = 1.208346456826E+01 kJ/mol
+
+print APOL energy 3 (solvated-cyclohexane) end
+  Global net APOL energy = 1.354016672221E+01 kJ/mol
+
+print APOL energy 4 (solvated-cyclopentane) end
+  Global net APOL energy = 9.363673200142E+00 kJ/mol
+
+print APOL energy 5 (solvated-ethane) end
+  Global net APOL energy = 9.422717598546E+00 kJ/mol
+
+print APOL energy 6 (solvated-hexane) end
+  Global net APOL energy = 1.640068943201E+01 kJ/mol
+
+print APOL energy 7 (solvated-isobutane) end
+  Global net APOL energy = 1.323144287435E+01 kJ/mol
+
+print APOL energy 8 (solvated-methane) end
+  Global net APOL energy = 7.894367190329E+00 kJ/mol
+
+print APOL energy 9 (solvated-neopentane) end
+  Global net APOL energy = 1.449633815052E+01 kJ/mol
+
+print APOL energy 10 (solvated-pentane) end
+  Global net APOL energy = 1.447900211546E+01 kJ/mol
+
+print APOL energy 11 (solvated-propane) end
+  Global net APOL energy = 1.192358496286E+01 kJ/mol
+----------------------------------------
+CLEANING UP AND SHUTTING DOWN...
+Destroying force arrays.
+No energy arrays to destroy.
+Destroying multigrid structures.
+Destroying finite element structures.
+Destroying 11 molecules
+Final memory usage:  0.001 MB total, 2.267 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/alkanes/apbs-forces.in

@@ -0,0 +1,24 @@
+read 
+	mol pdb pentane.pdb
+	parm flat parm.dat
+end
+
+APOLAR name solvated
+	grid 0.3 0.3 0.3
+	mol 1
+	srfm sacc
+	swin 0.3
+	srad 0.65
+	press 0.2394
+	gamma 0.0085
+	bconc 0.033428
+	sdens 100.0
+	dpos 0.2
+	temp 298.15
+	calcenergy total
+	calcforce comps
+END
+
+print apolForce solvated end
+
+quit