Upload folder using huggingface_hub (part 3)

.gitattributes

@@ -30,3 +30,18 @@ model/comp_surface/tools/transfer/APBS-3.4.1.Linux/lib/libmaloc.a filter=lfs dif
 model/comp_surface/tools/transfer/APBS-3.4.1.Linux/lib/libmc.a filter=lfs diff=lfs merge=lfs -text
 model/comp_surface/tools/transfer/APBS-3.4.1.Linux/lib/libsuperlu.a filter=lfs diff=lfs merge=lfs -text
 model/comp_surface/tools/transfer/APBS-3.4.1.Linux/lib/libvf2c.a filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/analysis filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/benchmark filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/born filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/coulomb filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/dx2mol filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/dx2uhbd filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/dxmath filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/mergedx filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/mergedx2 filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/mgmesh filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/multivalue filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/similarity filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/smooth filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/tools/bin/value filter=lfs diff=lfs merge=lfs -text
+model/comp_surface/tools/transfer/pdb2pqr-linux-bin64-2.1.1/doc/images/flowchart.png filter=lfs diff=lfs merge=lfs -text

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pbsam-gly/gly_cg2.pqr

@@ -0,0 +1,34 @@
+ATOM     34  C   CHG A1           8.257  13.181  10.022 -0.1550  1.8700
+ATOM     35  C   CHG A1           9.757  13.181  10.022  0.6500  1.8700
+ATOM     36  C   CHG A1          10.444  14.154  10.022 -0.5330  1.7600
+ATOM     37  C   CHG A1          10.239  11.942  10.033 -0.4280  1.5200
+ATOM     38  C   CHG A1          11.637  11.723  10.103  0.1240  1.8700
+ATOM     39  C   CHG A1          12.093  11.493  11.539  0.1220  1.8700
+ATOM     40  C   CHG A1          13.443  10.806  11.569  0.1430  1.8700
+ATOM     41  C   CHG A1          13.738  10.513  12.923 -0.4260  1.5200
+ATOM     42  C   CHG A1          14.898   9.923  13.184  0.6450  1.8700
+ATOM     43  C   CHG A1          15.083   9.690  14.656 -0.1550  1.8700
+ATOM     44  C   CHG A1          15.679   9.625  12.337 -0.5290  1.7600
+ATOM     45  C   CHG A1          12.252  12.735  12.209 -0.4260  1.5200
+ATOM     46  C   CHG A1          11.287  13.208  12.989  0.6560  1.8700
+ATOM     47  C   CHG A1          10.256  12.643  13.180 -0.5370  1.7600
+ATOM     48  C   CHG A1          11.662  14.541  13.569 -0.1540  1.8700
+ATOM     49  C   CHG A1           7.882  12.524   9.247  0.0670  1.1000
+ATOM     50  C   CHG A1           7.896  14.188   9.873  0.0720  1.1000
+ATOM     51  C   CHG A1           7.914  12.804  10.979  0.0800  1.1000
+ATOM     52  C   CHG A1          11.809  10.829   9.519  0.0730  1.1000
+ATOM     53  C   CHG A1          12.168  12.554   9.662  0.0740  1.1000
+ATOM     54  C   CHG A1          11.360  10.896  12.062  0.0900  1.1000
+ATOM     55  C   CHG A1          13.412   9.884  11.002  0.0550  1.1000
+ATOM     56  C   CHG A1          14.216  11.441  11.157  0.0630  1.1000
+ATOM     57  C   CHG A1          15.060  10.639  15.179  0.0690  1.1000
+ATOM     58  C   CHG A1          14.269   9.084  15.035  0.0690  1.1000
+ATOM     59  C   CHG A1          16.028   9.196  14.826  0.0730  1.1000
+ATOM     60  C   CHG A1          11.715  15.264  12.764  0.0790  1.1000
+ATOM     61  C   CHG A1          10.915  14.844  14.288  0.0710  1.1000
+ATOM     62  C   CHG A1          12.637  14.483  14.036  0.0680  1.1000
+ATOM     63  X   CEN A1          10.759  12.827  11.235  0.0000  3.9751
+ATOM     64  X   CEN A1          14.507  10.091  13.247  0.0000  3.6588
+ATOM     65  X   CEN A1          11.671  15.532  13.495  0.0000  2.8821
+ATOM     66  X   CEN A1           8.243  13.360  10.290  0.0000  3.5538
+ATOM     67  X   CEN A1          13.443  10.806  11.569  0.0000  1.8700

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pbsam-gly/gly_dynamics.in

@@ -0,0 +1,50 @@
+read
+   #mol pqr gly.pqr
+   #mol pqr gly2.pqr
+    mol pqr gly_cg.pqr
+    mol pqr gly_cg2.pqr
+end
+elec name comp_solv        # Gly
+    pbsam-auto
+
+    runtype dynamics        # Can be energyforce, electrostatics etc
+    runname dyn_gly         # Output name for files created by program
+
+    units kT
+    ## info for molecule
+    #mesh skin
+    tolsp 2.5
+
+   #imat imat/mol0sph
+   #imat imat/mol1sph
+
+   #exp exp/mol0
+   #exp exp/mol1
+
+    termcombine or
+    term time 560.0
+    ntraj 2
+
+    # WARN: diff with a number is not supported in pbsam-auto
+    # diff 1 move 0.45 0.001
+    diff move 0.45 0.001
+    # WARN: diff with a number is not supported in pbsam-auto
+    # diff 2 stat
+    diff stat
+
+    xyz 1 traj_1_1.xyz
+    xyz 1 traj_1_2.xyz
+
+    xyz 2 traj_2_1.xyz
+    xyz 2 traj_2_2.xyz
+
+    temp 298.15                                       # System temperature (K)
+    pdie 4.0                                          # Solute dielectric                 
+    sdie 80.0                                         # Solvent dielectric                
+    # WARN: ion is not supported in pbsam-auto
+    # ion charge 0.0 conc 0.05 radius 0.0               # Monovalent salt conc in M
+
+end
+
+quit
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pbsam-gly/gly_electrostatic.in

@@ -0,0 +1,32 @@
+read
+    mol pqr gly.pqr
+end
+elec name comp_solv        # Gly
+    pbsam-auto
+
+    runtype electrostatics  # Can be energyforce, electrostatics etc
+    runname elec_gly        # Output name for files created by program
+
+    units jmol
+    ## info for molecule
+    # WARN: mesh is not supported in pbsam-auto
+    # mesh skin
+    tolsp 2.5
+
+    temp 298.15                                       # System temperature (K)
+    pdie 4.0                                          # Solute dielectric                 
+    sdie 78.0                                         # Solvent dielectric                
+    # WARN: ion is not supported in pbsam-auto
+    # ion charge 0.0 conc 0.10 radius 0.0               # Monovalent salt conc in M
+
+    # WARN: dime is not supported in pbsam-auto
+    # dime 20
+    # WARN: write is not supported in pbsam-auto
+    # write pot dx gly_0.1M.dx
+    3dmap  gly_0.1M.map
+    grid2d gly_0.1M.x0.dat x 0.0
+
+end
+
+quit
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pbsam-gly/gly_energyforce.in

@@ -0,0 +1,33 @@
+read
+   #mol pqr gly.pqr
+   #mol pqr gly2.pqr
+    mol pqr gly_cg.pqr
+    mol pqr gly_cg2.pqr
+end
+elec name comp_solv        # Gly
+    pbsam-auto
+
+    runtype energyforce     # Can be energyforce, electrostatics etc
+    runname enfo_gly        # Output name for files created by program
+
+    units kT
+    ## info for molecule
+    #mesh skin
+    tolsp 2.5
+
+   #imat imat/mol0sph
+   #imat imat/mol1sph
+
+   #exp exp/mol0
+   #exp exp/mol1
+
+    temp 298.15                                       # System temperature (K)
+    pdie 4.0                                          # Solute dielectric                 
+    sdie 80.0                                         # Solvent dielectric                
+    # WARN: ion is not supported in pbsam-auto
+    # ion charge 0.0 conc 0.05 radius 0.0               # Monovalent salt conc in M
+
+end
+
+quit
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pbsam-gly/msms/gly_electrostatic.in

@@ -0,0 +1,31 @@
+read
+    mol pqr gly_msms.pqr
+end
+elec name comp_solv        # Gly
+    pbsam
+
+    runtype electrostatics  # Can be energyforce, electrostatics etc
+    runname elec_gly        # Output name for files created by program
+
+    units jmol
+    ## info for molecule
+    # WARN: mesh is not supported in pbsam-auto
+    # mesh skin
+    tolsp 2.5
+
+    temp 298.15                                       # System temperature (K)
+    pdie 4.0                                          # Solute dielectric                 
+    sdie 78.0                                         # Solvent dielectric                
+    # WARN: ion is not supported in pbsam-auto
+    # ion charge 0.0 conc 0.10 radius 0.0               # Monovalent salt conc in M
+
+    # WARN: dime is not supported in pbsam-auto
+    # dime 20
+    dx gly_0.1M.dx
+    3dmap  gly_0.1M.map
+    grid2d gly_0.1M.x0.dat x 0.0
+
+end
+
+quit
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pbsam-gly/msms/gly_msms.pqr

@@ -0,0 +1,29 @@
+ATOM       1    C   A  0        0.0000   0.0000   0.0000  -0.1550 1.8700   
+ATOM       2    C   A  0        1.5000   0.0000   0.0000   0.6500 1.8700   
+ATOM       3    O   A  0        2.1870   0.9730   0.0000  -0.5330 1.7600   
+ATOM       4    O   A  0        1.9820  -1.2390   0.0110  -0.4280 1.5200   
+ATOM       5    C   A  0        3.3800  -1.4580   0.0810   0.1240 1.8700   
+ATOM       6    C   A  0        3.8360  -1.6880   1.5170   0.1220 1.8700   
+ATOM       7    C   A  0        5.1860  -2.3750   1.5470   0.1430 1.8700   
+ATOM       8    O   A  0        5.4810  -2.6680   2.9010  -0.4260 1.5200   
+ATOM       9    C   A  0        6.6410  -3.2580   3.1620   0.6450 1.8700   
+ATOM      10    C   A  0        6.8260  -3.4910   4.6340  -0.1550 1.8700   
+ATOM      11    O   A  0        7.4220  -3.5560   2.3150  -0.5290 1.7600   
+ATOM      12    O   A  0        3.9950  -0.4460   2.1870  -0.4260 1.5200   
+ATOM      13    C   A  0        3.0300   0.0270   2.9670   0.6560 1.8700   
+ATOM      14    O   A  0        1.9990  -0.5380   3.1580  -0.5370 1.7600   
+ATOM      15    C   A  0        3.4050   1.3600   3.5470  -0.1540 1.8700   
+ATOM      16    H   A  0       -0.3750  -0.6570  -0.7750   0.0670 1.1000   
+ATOM      17    H   A  0       -0.3610   1.0070  -0.1490   0.0720 1.1000   
+ATOM      18    H   A  0       -0.3430  -0.3770   0.9570   0.0800 1.1000   
+ATOM      19    H   A  0        3.5520  -2.3520  -0.5030   0.0730 1.1000   
+ATOM      20    H   A  0        3.9110  -0.6270  -0.3600   0.0740 1.1000   
+ATOM      21    H   A  0        3.1030  -2.2850   2.0400   0.0900 1.1000   
+ATOM      22    H   A  0        5.1550  -3.2970   0.9800   0.0550 1.1000   
+ATOM      23    H   A  0        5.9590  -1.7400   1.1350   0.0630 1.1000   
+ATOM      24    H   A  0        6.8030  -2.5420   5.1570   0.0690 1.1000   
+ATOM      25    H   A  0        6.0120  -4.0970   5.0130   0.0690 1.1000   
+ATOM      26    H   A  0        7.7710  -3.9850   4.8040   0.0730 1.1000   
+ATOM      27    H   A  0        3.4580   2.0830   2.7420   0.0790 1.1000   
+ATOM      28    H   A  0        2.6580   1.6630   4.2660   0.0710 1.1000   
+ATOM      29    H   A  0        4.3800   1.3020   4.0140   0.0680 1.1000   

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pbsam-gly/traj_1_1.xyz

@@ -0,0 +1 @@
+  0.0 0.0 0.0

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pbsam-gly/traj_1_2.xyz

@@ -0,0 +1 @@
+ 10.0 10.0 10.0

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pbsam-gly/traj_2_1.xyz

@@ -0,0 +1 @@
+ -15.0 -15.0 -15.0

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pbsam-gly/traj_2_2.xyz

@@ -0,0 +1 @@
+ -5.0 -5.0 -5.0

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

@@ -0,0 +1,103 @@
+README for pka-lig APBS examples
+================================
+
+The example input files in this directory calculate the binding energes of a ligand to protein kinase A.
+
+This example was contributed by Chung Wong.
+
+Input File|Description|APBS Version|Results (kJ/mol)|UHBD (kJ/mol)
+---|---|---|---|---
+[apbs-mol-vdw.in](apbs-mol-vdw.in)|2-level focusing to 0.250 A spacing, VdW surface, srfm mol|**1.5**|**8.08352**|8.876
+|||1.4.2|8.08352
+|||1.4.1|8.0835
+|||1.4|8.0835
+|||1.3|8.0835
+|||1.2.1|8.0835
+|||1.2|8.0835<sup>[4](#4)</sup>
+|||1.1.0|8.0858
+|||1.0.0|8.0858
+|||0.5.1|8.0858<sup>[3](#3)</sup>
+|||0.5.0|8.0640
+||||0.4.0|8.0640
+[apbs-smol-vdw.in](apbs-smol-vdw.in)|2-level focusing to 0.250 A spacing, VdW surface, srfm smol|**1.5**|**20.9630**|8.876
+|||1.4.2|20.9630
+|||1.4.1|20.9630
+|||1.4|20.9630
+|||1.3|20.9630
+|||1.2.1|20.9630
+|||1.2|20.9630<sup>[4](#4)</sup>
+|||1.1.0|20.9628
+|||1.0.0|20.9628
+|||0.5.1|20.9628<sup>[3](#2)</sup>
+|||0.5.0|20.9542
+|||0.4.0|20.9542<sup>[2](#2)</sup>
+|||0.3.2|8.0640<sup>[1](#1)</sup>
+|||0.3.1|6.6465
+|||0.3.0|6.6465
+|||0.2.6|6.6465
+|||0.2.5|6.6465
+|||0.2.4|6.6465
+|||0.2.3|6.6465
+|||0.2.2|6.6465
+|||0.2.1|6.647
+|||0.2.0|6.647
+|||0.1.8|6.65
+[apbs-mol-surf.in](apbs-mol-surf.in)|2-level focusing to 0.250 A spacing, molecular surface, srfm mol|**1.5**|**119.2610**|86.50
+|||1.4.2|119.2610
+|||1.4.1|119.2608
+|||1.4|119.2608
+|||1.3|119.2608
+|||1.2.1|119.2608
+|||1.2|119.2608<sup>[4](#4)</sup>
+|||1.1.0|119.2607
+|||1.0.0|119.2607
+|||0.5.1|119.2607<sup>[3](#3)</sup>
+|||0.5.0|119.2347
+|||0.4.0|119.2347
+[apbs-smol-surf.in](apbs-smol-surf.in)|2-level focusing to 0.250 A spacing, molecular surface, srfm smol|**1.5**|**108.8770**|86.50
+|||1.4.2|108.8770
+|||1.4.1|108.8773
+|||1.4|108.8773<sup>[5](#5)</sup>
+|||1.3|108.8748
+|||1.2.1|108.8748
+|||1.2|108.8748<sup>[4](#4)</sup>
+|||1.1.0|108.8773
+|||1.0.0|108.8773
+|||0.5.1|108.8773<sup>[3](#3)</sup>
+|||0.5.0|108.8540
+|||0.4.0|108.8540<sup>[2](#2)</sup>
+|||0.3.2|94.8705<sup>[1](#1)</sup>
+|||0.3.1|97.0147
+|||0.3.0|97.0147
+|||0.2.6|97.0147
+|||0.2.5|97.0147
+|||0.2.4|97.0147
+|||0.2.3|97.0147
+|||0.2.2|97.0147
+|||0.2.1|97.015
+|||0.2.0|97.015
+|||0.1.8|97.01
+
+<a name=1></a><sup>1</sup> The grid dimensions (dime) changed from 65\^3 to 97\^3 in the 0.3.2 release to give a finer mesh.
+
+<a name=2></a><sup>2</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=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> 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=5></a><sup>5</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/pka-lig/UHBD/README

@@ -0,0 +1,22 @@
+The calculations were done two ways:
+
+UHBD1 ==> molecular surface-baed dielectric definition
+
+  The files uhbd1-bin.out, uhbd1-apo.out, and uhbd1-lig.out contain the
+  total electrostatic energies for the complex, apo protein, and ligand
+  respectively.  Subtracting the apo and ligand energies from the
+  complex energy gives the change binding energy:
+
+    DGbind = 161106.68491555 - 159047.22267973 - 2038.8019114004 kcal/mol
+           = 20.660 kcal/mol = 86.50 kJ/mol
+
+UHBD2 ==> van der Waals-based dielectric definition
+
+  The files uhbd2-bin.out, uhbd2-apo.out, and uhbd2-lig.out contain the
+  total electrostatic energies for the complex, apo protein, and ligand
+  respectively.  Subtracting the apo and ligand energies from the
+  complex energy gives the change binding energy:
+
+    DGbind = 160097.85343977 - 158065.92915468 - 2029.8041091354 kcal/mol
+           = 2.120 kcal/mol = 8.876 kJ/mol
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pka-lig/UHBD/uhbd1-lig.out

@@ -0,0 +1,281 @@
+
+
+ UNIVERSITY OF HOUSTON BROWNIAN DYNAMICS  (Release experimental)
+
+   AUTHORS                 : Jeffry Madura
+                           : Malcolm Davis
+                           : Rebecca Wade
+                           : Brock Luty
+                           : Michael Gilson
+                           : Jan Antosiewicz
+
+   date/time               : 28-Jan-   2  12:26:49 CST
+
+
+ CURRENT MAXIMUM PROGRAM DIMENSIONS     
+   Maximum Number of Atoms                           :     20000
+   Maximum Grid Size                                 :       250^3 
+   Maximum Number of Subunits                        :        40
+   Maximum Entries in Atomic Database                :      1500
+   Maximum Equivalences in Atomic Database           :      1000
+   Maximum Number of Runs                            :      1000
+   Maximum Number of Reaction Sites                  :        40
+   Maximum Number of Criteria per Reaction Site      :        10
+   Maximum Number of Columns in an Atomic Database   :        16
+   Maximum Number of Diffusing Units                 :         5
+   Maximum Number of Diffusing Subunits              :        15
+   Maximum Number of Distance Constraints            :        30
+   Maximum Number of Molecules                       :        50
+   Maximum Number of Time Step Regions               :         5
+   Maximum Number of Time Steps for Correlation Func.:        11
+   Maximum Number of Bins for Dihedral Distributions :       360
+   Maximum Number of Trajectories for Analysis       :         1
+   Maximum Number of Traj. Files to be Concatenated  :        10
+   Maximum Number of User Variables                  :      1500
+   Maximum Number of Atom Neighbors                  :       300
+   Maximum Number of Surface Points per Atom         :      5000
+   Maximum Number of S+R Surface Points              :    100000
+   Maximum Number of Elements in the C{eval} Stack  :        20
+   Maximum Number of Blocks for Gaussian Random #s   :      1000
+   Maximum Vector length for Vector Processor        :      1024
+   Maximum Number of 1-2 and 1-3 Atom Exclusions     :        20
+   Maximum Number of 1-4 Interactions per Atom       :        40
+   Maximum Number of Bond+Nonbond Interact. per Atom :        20
+   Maximum Number of Bonds                           :      6000
+   Maximum Number of Angles                          :      6000
+   Maximum Number of Dihedrals                       :      8000
+   Maximum Size of the Nonbonded List                :   7000000
+
+
+Main >  
+Main >  read mol 1 file "./bx6_7_lig.pdb" pdb end
+
+ READ MODULE
+ READ COORDINATES
+   Molecule number                                   :         1
+   Coordinate file                                   :./bx6_7_lig.pdb     
+   File format                                       :free format PDB     
+   Atoms read                                        :        47
+
+
+Main >  rdtop new file "./bx6_lig.top" mol 1 end
+./bx6_lig.top                                                                   
+ WARNING:
+Radii have been assigned from topology  file.
+ To change this, read radii after topology file
+
+Main >  set radii file "/net/home/cwong/PKA/charmm.uhb" para "charmm_rmin" end
+ SET MODULE
+   Setting                                           :               radii
+   Parameter set                                     :charmm_rmin         
+   Database file                                     :/net/home/cwong/PKA/
+   Reading of database completed                     :
+   Number of entries                                 :      1459
+   Number of equivalences                            :         0
+   Assignments made                                  :        47
+Main >  
+Main >  print apar mol 1 end
+
+ PRINT MODULE     
+ PRINTING ATOMIC PARAMETER INFORMATION   
+     Atom    Residue       Coordinates(x,y,z)      Charge   Radii   Net Charge
+     1 c1   bx6    351   22.758  -32.646   24.883    0.550    1.870
+     2 c8   bx6    351   21.510  -33.006   25.576    0.000    2.040
+     3 c9   bx6    351   21.396  -34.314   26.095    0.000    1.990
+     4 c10  bx6    351   20.219  -34.702   26.754    0.000    1.990
+     5 c11  bx6    351   19.169  -33.770   26.877    0.250    2.040
+     6 o1   bx6    351   17.998  -34.158   27.496   -0.650    1.550
+     7 c12  bx6    351   19.279  -32.456   26.383    0.000    1.990
+     8 c13  bx6    351   20.457  -32.073   25.721    0.000    1.990
+     9 o2   bx6    351   23.656  -33.453   24.670   -0.550    1.550
+    10 n2   bx6    351   22.872  -31.357   24.491   -0.350    1.830
+    11 n1   bx6    351   26.155  -29.614   24.198   -0.300    1.650
+    12 c2   bx6    351   24.835  -29.952   24.746    0.300    2.235
+    13 c3   bx6    351   24.113  -30.950   23.837    0.100    2.265
+    14 c4   bx6    351   23.795  -30.459   22.416    0.250    2.265
+    15 c5   bx6    351   23.954  -28.951   22.169    0.000    2.235
+    16 c6   bx6    351   25.401  -28.443   22.138    0.000    2.235
+    17 c7   bx6    351   26.083  -28.320   23.505    0.300    2.235
+    18 o3   bx6    351   24.606  -31.211   21.456   -0.550    1.600
+    19 c14  bx6    351   24.157  -31.482   20.238    0.700    1.870
+    20 o4   bx6    351   23.102  -31.107   19.824   -0.400    1.520
+    21 c15  bx6    351   25.053  -32.334   19.447    0.000    2.040
+    22 c16  bx6    351   24.584  -32.927   18.272    0.000    1.990
+    23 c17  bx6    351   25.397  -33.802   17.546    0.250    2.040
+    24 o5   bx6    351   24.862  -34.331   16.386   -0.650    1.550
+    25 c18  bx6    351   26.691  -34.119   18.005    0.000    2.040
+    26 c19  bx6    351   27.171  -33.490   19.175    0.250    2.040
+    27 o6   bx6    351   28.416  -33.747   19.715   -0.650    1.550
+    28 c20  bx6    351   26.362  -32.582   19.867    0.000    1.990
+    29 c21  bx6    351   27.475  -35.140   17.267    0.400    1.870
+    30 o7   bx6    351   26.946  -35.882   16.448   -0.400    1.550
+    31 c22  bx6    351   28.916  -35.270   17.535    0.000    2.040
+    32 c23  bx6    351   29.344  -36.371   18.289    0.250    2.040
+    33 o8   bx6    351   28.427  -37.285   18.770   -0.650    1.550
+    34 c24  bx6    351   30.703  -36.559   18.569    0.000    1.990
+    35 c25  bx6    351   31.646  -35.633   18.114    0.000    1.990
+    36 c26  bx6    351   31.224  -34.528   17.366    0.000    1.990
+    37 c27  bx6    351   29.864  -34.340   17.054    0.000    2.040
+    38 c28  bx6    351   29.480  -33.190   16.214    0.140    1.870
+    39 o9   bx6    351   30.052  -32.107   16.355   -0.570    1.660
+    40 o10  bx6    351   28.595  -33.344   15.376   -0.570    1.660
+    41 h1   bx6    351   18.044  -35.081   27.714    0.400    0.760
+    42 h2   bx6    351   22.142  -30.695   24.663    0.250    0.800
+    43 h3   bx6    351   26.483  -30.339   23.572    0.350    0.800
+    44 h4   bx6    351   25.537  -34.741   15.864    0.400    0.760
+    45 h5   bx6    351   28.438  -33.485   20.628    0.400    0.760
+    46 h6   bx6    351   28.878  -37.986   19.224    0.400    0.760
+    47 h7   bx6    351   26.819  -29.545   24.959    0.350    0.800    0.000
+ Center of Geometry of this list of Atoms(x,y,z)
+                         25.384  -33.006   21.189
+ Total Charge of this list of Atoms
+                          0.000
+
+
+Main >  print upar mol 1 end
+
+ PRINT MODULE     
+ PRINTING UNIT PARAMETER INFORMATION  
+ Unit  First/Last       Number of            subunit   atoms at
+        subunits    subs  bonds angls dihed  at cog    cent of subs
+
+
+Main >  print geom all  end
+
+ PRINT MODULE     
+ PRINTING GEOMETRICAL QUANTITIES FOR ATOMS
+ GEOMETRY ANALYSIS OF ATOM LIST                    
+   Center of geometry of atoms at (x,y,z)            :  25.384, -33.006,  21.189
+ Max distance of any atom coord from center of geom:  10.03826
+   Xmin, Xmax, Xmax-Xmin                             :  16.448,  33.636,  17.188
+   Ymin, Ymax, Ymax-Ymin                             : -38.835, -26.085,  12.750
+   Zmin, Zmax, Zmax-Zmin                             :  13.716,  29.046,  15.330
+   Maximum number of grid points available (per edge):     250
+   Grid unit spacing, Grid unit volume(x1000)        :   0.070,   0.341
+   Grid origin (of Octant)                           :  16.651, -41.740,  12.455
+   Substrate exclusion radius              (srad #.#):   0.000
+   Volume of molecule based on excluded volume       :   539.1
+   Effective Radius based on excluded volume         :   5.049
+ DOING RADIAL ANALYSIS OF ATOM LIST                
+   Distance between radial steps           (rdel #.#):   1.000
+   Number of cosine theta intervals        (ncos #.#):      50
+   Number of phi intervals                 (nphi #.#):     100
+   Minimum radius found                              :   1.000
+   Maximum radius found                              :  11.000
+   Average radius                                    :   3.993      +/-    2.390
+   number of holes encounter stepping in r coord     :    662.
+
+
+Main >  
+Main >  ! FINAL on NCSA computers
+Main >  elec calc mol 1 bcfl 2 grid 0.3 dime 240 240 240 maxits 500
+Elec >       pdie 2 sdie 78 gcenter 28.99    -29.75     29.57 nmap 1.4 end
+ ELECTROSTATIC MODULE
+ GRID CONSTANTS
+   Grid dimensioned to                   (same dime) :         user values
+   Grid dimensions                      (dime # # #) :240,240,240
+   Grid located by   (gcen,gcor,cent,same orig,gori) :   center specified.
+   Grid origin (range (min,max))                     :    -7.160  A        64.840  A
+                                                         -65.900  A         6.100  A
+                                                          -6.580  A        65.420  A
+   Grid spacing set to                   (same dime) :         user values
+   Grid spacing                           (grid #.#) :     0.300  A
+   Do analytic potential calculation     (no/analyt) :         F
+ DIELECTRIC MAP DEFINITIONS
+ Use probe-accessible surface definition (newmap, & nnewmap):T F
+   Solvent probe radius:   1.40000
+   Number of surface points per atom sphere:       200
+   Utilize dielectric boundary smoothing (no/smooth) :         T
+ BOUNDARY CONDITION CONSTANTS
+   Boundary condition flag                  (bcfl #) :         2
+     - sum of atoms as independent DH spheres
+ ENVIRONMENTAL CONSTANTS
+   Interior dielectric constant           (pdie #.#) :     2.000
+   Interior permittivity                             :0.1146E-05 e^2ps^2/amuA^3
+   Solvent dielectric constant            (sdie #.#) :    78.000
+   Solvent permittivity                              :0.4468E-04 e^2ps^2/amuA^3
+   Temperature                            (temp #.#) :   300.000  K
+   Ionic strength                         (ions #.#) :     0.000  mM
+   Concentration  of monovalent cations (ions1p #.#) :     0.000  mM
+   Concentration  of   divalent cations (ions2p #.#) :     0.000  mM
+   Concentration  of  trivalent cations (ions3p #.#) :     0.000  mM
+   Concentration  of monovalent anions  (ions1n #.#) :     0.000  mM
+   Concentration  of   divalent anions  (ions2n #.#) :     0.000  mM
+   Concentration  of  trivalent anions  (ions3n #.#) :     0.000  mM
+   Debye-Huckel parameter                            :     0.000  1/A
+ ATOM SELECTION
+   Number of atoms selected                (mol#...) :        47
+   X-coordinate of the center of geometry            :    25.384    A
+   Y-coordinate of the center of geometry            :   -33.006    A
+   Z-coordinate of the center of geometry            :    21.189    A
+   Net charge of the selected atoms                  :     0.000    e
+   Effective radius of the selected atoms            :     1.870    A
+ ITERATION VALUES
+   Maximum iterations                       (maxi #) :       500
+   Convergence criteria                   (conv #.#) :0.1000E-05
+   Linear equation solver flag              (solv #) :         1
+     - incomplete Cholesky preconditioned conjugate gradient
+ PERFORMING SETUP AND CALCULATION
+ Number of surface points:    1140
+ ASSIGNMENT
+   Set the variable:                area1             = 0.26851690751314E+03
+ ASSIGNMENT
+   Set the variable:                area2             = 0.82282238185406E+03
+ rprobe:   1.400000    
+ VDW contact surface area in srsrf:         268.517
+ PROBE-CENTER surface area in srsrf:        822.822
+ ITERATION SUMMARY
+   Iterations required                               :         1
+   Norm of the constant vector                       :0.1125E+03
+   Norm of the residual vector                       :0.1115E-03
+   Convergence achieved                              :0.9910E-06
+Main >  print elec zenerg mol 1 end
+
+ PRINT MODULE     
+ PRINTING ELECTROSTATICS
+
+
+Main >  print elec energy mol 1 end
+
+ PRINT MODULE     
+ PRINTING ELECTROSTATICS
+   Electrostatic energy for selected atoms           :0.203880E+04 kcal/mol
+ ASSIGNMENT
+   Set the variable:               energy             = 0.20388019114004E+04
+
+
+Main >  print elec self mol 1 end
+
+ PRINT MODULE     
+ PRINTING ELECTROSTATICS
+   Electrostatic self energy for selected atoms      :0.251476E+04 kcal/mol
+ ASSIGNMENT
+   Set the variable:                 self             = 0.25147570607692E+04
+
+
+Main >  print elec fdcoul mol 1 end
+
+ PRINT MODULE     
+ PRINTING ELECTROSTATICS
+   Electrostatic finite-difference Coulombic energy  :-.407057E+03 kcal/mol
+ ASSIGNMENT
+   Set the variable:               fdcoul             = -.40705748848414E+03
+
+
+Main >  print elec tenerg mol 1 end
+
+ PRINT MODULE     
+ PRINTING ELECTROSTATICS
+   Summed energy terms for selected atoms            :-.688977E+02 kcal/mol
+ ASSIGNMENT
+   Set the variable:              tenergy             = -.68897660884674E+02
+
+
+Main >  
+Main >  stop
+ UHBD termination
+   date/time               : 28-Jan-   2  13:09:29 CST
+   total CPU seconds       :   2455.698
+ total usr/sys CPU seconds :   2442.887/    12.811
+
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pka-lig/UHBD/uhbd2-lig.out

@@ -0,0 +1,270 @@
+
+
+ UNIVERSITY OF HOUSTON BROWNIAN DYNAMICS  (Release experimental)
+
+   AUTHORS                 : Jeffry Madura
+                           : Malcolm Davis
+                           : Rebecca Wade
+                           : Brock Luty
+                           : Michael Gilson
+                           : Jan Antosiewicz
+
+   date/time               : 26-Jan-   2  21:17:02 CST
+
+
+ CURRENT MAXIMUM PROGRAM DIMENSIONS     
+   Maximum Number of Atoms                           :     20000
+   Maximum Grid Size                                 :       250^3 
+   Maximum Number of Subunits                        :        40
+   Maximum Entries in Atomic Database                :      1500
+   Maximum Equivalences in Atomic Database           :      1000
+   Maximum Number of Runs                            :      1000
+   Maximum Number of Reaction Sites                  :        40
+   Maximum Number of Criteria per Reaction Site      :        10
+   Maximum Number of Columns in an Atomic Database   :        16
+   Maximum Number of Diffusing Units                 :         5
+   Maximum Number of Diffusing Subunits              :        15
+   Maximum Number of Distance Constraints            :        30
+   Maximum Number of Molecules                       :        50
+   Maximum Number of Time Step Regions               :         5
+   Maximum Number of Time Steps for Correlation Func.:        11
+   Maximum Number of Bins for Dihedral Distributions :       360
+   Maximum Number of Trajectories for Analysis       :         1
+   Maximum Number of Traj. Files to be Concatenated  :        10
+   Maximum Number of User Variables                  :      1500
+   Maximum Number of Atom Neighbors                  :       300
+   Maximum Number of Surface Points per Atom         :      5000
+   Maximum Number of S+R Surface Points              :    100000
+   Maximum Number of Elements in the C{eval} Stack  :        20
+   Maximum Number of Blocks for Gaussian Random #s   :      1000
+   Maximum Vector length for Vector Processor        :      1024
+   Maximum Number of 1-2 and 1-3 Atom Exclusions     :        20
+   Maximum Number of 1-4 Interactions per Atom       :        40
+   Maximum Number of Bond+Nonbond Interact. per Atom :        20
+   Maximum Number of Bonds                           :      6000
+   Maximum Number of Angles                          :      6000
+   Maximum Number of Dihedrals                       :      8000
+   Maximum Size of the Nonbonded List                :   7000000
+
+
+Main >  
+Main >  read mol 1 file "./bx6_7_lig.pdb" pdb end
+
+ READ MODULE
+ READ COORDINATES
+   Molecule number                                   :         1
+   Coordinate file                                   :./bx6_7_lig.pdb     
+   File format                                       :free format PDB     
+   Atoms read                                        :        47
+
+
+Main >  rdtop new file "./bx6_lig.top" mol 1 end
+./bx6_lig.top                                                                   
+ WARNING:
+Radii have been assigned from topology  file.
+ To change this, read radii after topology file
+
+Main >  set radii file "/net/home/cwong/PKA/charmm.uhb" para "charmm_rmin" end
+ SET MODULE
+   Setting                                           :               radii
+   Parameter set                                     :charmm_rmin         
+   Database file                                     :/net/home/cwong/PKA/
+   Reading of database completed                     :
+   Number of entries                                 :      1459
+   Number of equivalences                            :         0
+   Assignments made                                  :        47
+Main >  
+Main >  print apar mol 1 end
+
+ PRINT MODULE     
+ PRINTING ATOMIC PARAMETER INFORMATION   
+     Atom    Residue       Coordinates(x,y,z)      Charge   Radii   Net Charge
+     1 c1   bx6    351   22.758  -32.646   24.883    0.550    1.870
+     2 c8   bx6    351   21.510  -33.006   25.576    0.000    2.040
+     3 c9   bx6    351   21.396  -34.314   26.095    0.000    1.990
+     4 c10  bx6    351   20.219  -34.702   26.754    0.000    1.990
+     5 c11  bx6    351   19.169  -33.770   26.877    0.250    2.040
+     6 o1   bx6    351   17.998  -34.158   27.496   -0.650    1.550
+     7 c12  bx6    351   19.279  -32.456   26.383    0.000    1.990
+     8 c13  bx6    351   20.457  -32.073   25.721    0.000    1.990
+     9 o2   bx6    351   23.656  -33.453   24.670   -0.550    1.550
+    10 n2   bx6    351   22.872  -31.357   24.491   -0.350    1.830
+    11 n1   bx6    351   26.155  -29.614   24.198   -0.300    1.650
+    12 c2   bx6    351   24.835  -29.952   24.746    0.300    2.235
+    13 c3   bx6    351   24.113  -30.950   23.837    0.100    2.265
+    14 c4   bx6    351   23.795  -30.459   22.416    0.250    2.265
+    15 c5   bx6    351   23.954  -28.951   22.169    0.000    2.235
+    16 c6   bx6    351   25.401  -28.443   22.138    0.000    2.235
+    17 c7   bx6    351   26.083  -28.320   23.505    0.300    2.235
+    18 o3   bx6    351   24.606  -31.211   21.456   -0.550    1.600
+    19 c14  bx6    351   24.157  -31.482   20.238    0.700    1.870
+    20 o4   bx6    351   23.102  -31.107   19.824   -0.400    1.520
+    21 c15  bx6    351   25.053  -32.334   19.447    0.000    2.040
+    22 c16  bx6    351   24.584  -32.927   18.272    0.000    1.990
+    23 c17  bx6    351   25.397  -33.802   17.546    0.250    2.040
+    24 o5   bx6    351   24.862  -34.331   16.386   -0.650    1.550
+    25 c18  bx6    351   26.691  -34.119   18.005    0.000    2.040
+    26 c19  bx6    351   27.171  -33.490   19.175    0.250    2.040
+    27 o6   bx6    351   28.416  -33.747   19.715   -0.650    1.550
+    28 c20  bx6    351   26.362  -32.582   19.867    0.000    1.990
+    29 c21  bx6    351   27.475  -35.140   17.267    0.400    1.870
+    30 o7   bx6    351   26.946  -35.882   16.448   -0.400    1.550
+    31 c22  bx6    351   28.916  -35.270   17.535    0.000    2.040
+    32 c23  bx6    351   29.344  -36.371   18.289    0.250    2.040
+    33 o8   bx6    351   28.427  -37.285   18.770   -0.650    1.550
+    34 c24  bx6    351   30.703  -36.559   18.569    0.000    1.990
+    35 c25  bx6    351   31.646  -35.633   18.114    0.000    1.990
+    36 c26  bx6    351   31.224  -34.528   17.366    0.000    1.990
+    37 c27  bx6    351   29.864  -34.340   17.054    0.000    2.040
+    38 c28  bx6    351   29.480  -33.190   16.214    0.140    1.870
+    39 o9   bx6    351   30.052  -32.107   16.355   -0.570    1.660
+    40 o10  bx6    351   28.595  -33.344   15.376   -0.570    1.660
+    41 h1   bx6    351   18.044  -35.081   27.714    0.400    0.760
+    42 h2   bx6    351   22.142  -30.695   24.663    0.250    0.800
+    43 h3   bx6    351   26.483  -30.339   23.572    0.350    0.800
+    44 h4   bx6    351   25.537  -34.741   15.864    0.400    0.760
+    45 h5   bx6    351   28.438  -33.485   20.628    0.400    0.760
+    46 h6   bx6    351   28.878  -37.986   19.224    0.400    0.760
+    47 h7   bx6    351   26.819  -29.545   24.959    0.350    0.800    0.000
+ Center of Geometry of this list of Atoms(x,y,z)
+                         25.384  -33.006   21.189
+ Total Charge of this list of Atoms
+                          0.000
+
+
+Main >  print upar mol 1 end
+
+ PRINT MODULE     
+ PRINTING UNIT PARAMETER INFORMATION  
+ Unit  First/Last       Number of            subunit   atoms at
+        subunits    subs  bonds angls dihed  at cog    cent of subs
+
+
+Main >  print geom all  end
+
+ PRINT MODULE     
+ PRINTING GEOMETRICAL QUANTITIES FOR ATOMS
+ GEOMETRY ANALYSIS OF ATOM LIST                    
+   Center of geometry of atoms at (x,y,z)            :  25.384, -33.006,  21.189
+ Max distance of any atom coord from center of geom:  10.03826
+   Xmin, Xmax, Xmax-Xmin                             :  16.448,  33.636,  17.188
+   Ymin, Ymax, Ymax-Ymin                             : -38.835, -26.085,  12.750
+   Zmin, Zmax, Zmax-Zmin                             :  13.716,  29.046,  15.330
+   Maximum number of grid points available (per edge):     250
+   Grid unit spacing, Grid unit volume(x1000)        :   0.070,   0.341
+   Grid origin (of Octant)                           :  16.651, -41.740,  12.455
+   Substrate exclusion radius              (srad #.#):   0.000
+   Volume of molecule based on excluded volume       :   539.1
+   Effective Radius based on excluded volume         :   5.049
+ DOING RADIAL ANALYSIS OF ATOM LIST                
+   Distance between radial steps           (rdel #.#):   1.000
+   Number of cosine theta intervals        (ncos #.#):      50
+   Number of phi intervals                 (nphi #.#):     100
+   Minimum radius found                              :   1.000
+   Maximum radius found                              :  11.000
+   Average radius                                    :   3.993      +/-    2.390
+   number of holes encounter stepping in r coord     :    662.
+
+
+Main >  
+Main >  ! FINAL on NCSA computers
+Main >  elec calc mol 1 bcfl 2 grid 0.3 dime 240 240 240 maxits 500
+Elec >       pdie 2 sdie 78 gcenter 28.99    -29.75     29.57 end
+ ELECTROSTATIC MODULE
+ GRID CONSTANTS
+   Grid dimensioned to                   (same dime) :         user values
+   Grid dimensions                      (dime # # #) :240,240,240
+   Grid located by   (gcen,gcor,cent,same orig,gori) :   center specified.
+   Grid origin (range (min,max))                     :    -7.160  A        64.840  A
+                                                         -65.900  A         6.100  A
+                                                          -6.580  A        65.420  A
+   Grid spacing set to                   (same dime) :         user values
+   Grid spacing                           (grid #.#) :     0.300  A
+   Do analytic potential calculation     (no/analyt) :         F
+ DIELECTRIC MAP DEFINITIONS
+ Use probe-accessible surface definition (newmap, & nnewmap):F F
+   Utilize dielectric boundary smoothing (no/smooth) :         T
+ BOUNDARY CONDITION CONSTANTS
+   Boundary condition flag                  (bcfl #) :         2
+     - sum of atoms as independent DH spheres
+ ENVIRONMENTAL CONSTANTS
+   Interior dielectric constant           (pdie #.#) :     2.000
+   Interior permittivity                             :0.1146E-05 e^2ps^2/amuA^3
+   Solvent dielectric constant            (sdie #.#) :    78.000
+   Solvent permittivity                              :0.4468E-04 e^2ps^2/amuA^3
+   Temperature                            (temp #.#) :   300.000  K
+   Ionic strength                         (ions #.#) :     0.000  mM
+   Concentration  of monovalent cations (ions1p #.#) :     0.000  mM
+   Concentration  of   divalent cations (ions2p #.#) :     0.000  mM
+   Concentration  of  trivalent cations (ions3p #.#) :     0.000  mM
+   Concentration  of monovalent anions  (ions1n #.#) :     0.000  mM
+   Concentration  of   divalent anions  (ions2n #.#) :     0.000  mM
+   Concentration  of  trivalent anions  (ions3n #.#) :     0.000  mM
+   Debye-Huckel parameter                            :     0.000  1/A
+ ATOM SELECTION
+   Number of atoms selected                (mol#...) :        47
+   X-coordinate of the center of geometry            :    25.384    A
+   Y-coordinate of the center of geometry            :   -33.006    A
+   Z-coordinate of the center of geometry            :    21.189    A
+   Net charge of the selected atoms                  :     0.000    e
+   Effective radius of the selected atoms            :     1.870    A
+ ITERATION VALUES
+   Maximum iterations                       (maxi #) :       500
+   Convergence criteria                   (conv #.#) :0.1000E-05
+   Linear equation solver flag              (solv #) :         1
+     - incomplete Cholesky preconditioned conjugate gradient
+ PERFORMING SETUP AND CALCULATION
+ ITERATION SUMMARY
+   Iterations required                               :         1
+   Norm of the constant vector                       :0.1125E+03
+   Norm of the residual vector                       :0.1119E-03
+   Convergence achieved                              :0.9944E-06
+Main >  print elec zenerg mol 1 end
+
+ PRINT MODULE     
+ PRINTING ELECTROSTATICS
+
+
+Main >  print elec energy mol 1 end
+
+ PRINT MODULE     
+ PRINTING ELECTROSTATICS
+   Electrostatic energy for selected atoms           :0.202980E+04 kcal/mol
+ ASSIGNMENT
+   Set the variable:               energy             = 0.20298041091354E+04
+
+
+Main >  print elec self mol 1 end
+
+ PRINT MODULE     
+ PRINTING ELECTROSTATICS
+   Electrostatic self energy for selected atoms      :0.251476E+04 kcal/mol
+ ASSIGNMENT
+   Set the variable:                 self             = 0.25147570607692E+04
+
+
+Main >  print elec fdcoul mol 1 end
+
+ PRINT MODULE     
+ PRINTING ELECTROSTATICS
+   Electrostatic finite-difference Coulombic energy  :-.407057E+03 kcal/mol
+ ASSIGNMENT
+   Set the variable:               fdcoul             = -.40705748848414E+03
+
+
+Main >  print elec tenerg mol 1 end
+
+ PRINT MODULE     
+ PRINTING ELECTROSTATICS
+   Summed energy terms for selected atoms            :-.778955E+02 kcal/mol
+ ASSIGNMENT
+   Set the variable:              tenergy             = -.77895463149641E+02
+
+
+Main >  
+Main >  
+Main >  stop
+ UHBD termination
+   date/time               : 26-Jan-   2  22:43:41 CST
+
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pka-lig/apbs-mol-surf.in

@@ -0,0 +1,146 @@
+##########################################################################
+# PROTEIN KINASE INHIBITOR BINDING ENERGY -- MOLECULAR SURFACE
+##########################################################################
+
+read 
+    mol pqr bx6_7_lig_apbs.pqr
+    mol pqr bx6_7_apo_apbs.pqr
+    mol pqr bx6_7_bin_apbs.pqr
+end
+
+# LIGAND ENERGY (FOCUSING)
+elec name lig-coarse
+    mg-manual
+    dime 97 97 97 
+    glen 70 70 70
+    gcent mol 3
+    mol 1
+    lpbe
+    bcfl sdh
+    ion charge 1 conc 0.000 radius 2.0     
+    ion charge -1 conc 0.000 radius 2.0      
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm mol
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+elec name lig-fine
+    mg-manual
+    dime 97 97 97
+    grid 0.25 0.25 0.25
+    gcent mol 1
+    mol 1
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.000 radius 2.0     
+    ion charge -1 conc 0.000 radius 2.0        
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm mol
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# KINASE ENERGY (FOCUSING)
+elec name pka-coarse
+    mg-manual
+    dime 97 97 97
+    glen 70 70 70
+    gcent mol 3
+    mol 2
+    lpbe
+    bcfl sdh
+    ion charge 1 conc 0.000 radius 2.0     
+    ion charge -1 conc 0.000 radius 2.0    
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm mol
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+elec name pka-fine
+    mg-manual
+    dime 97 97 97
+    grid 0.25 0.25 0.25
+    gcent mol 1
+    mol 2
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.000 radius 2.0     
+    ion charge -1 conc 0.000 radius 2.0    
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm mol
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# COMPLEX ENERGY (FOCUSING)
+elec name complex-coarse
+    mg-manual
+    dime 97 97 97
+    glen 70 70 70
+    gcent mol 3
+    mol 3
+    lpbe
+    bcfl sdh
+    ion charge 1 conc 0.000 radius 2.0
+    ion charge -1 conc 0.000 radius 2.0
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm mol
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+elec name complex-fine
+    mg-manual
+    dime 97 97 97
+    grid 0.25 0.25 0.25
+    gcent mol 1
+    mol 3
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.000 radius 2.0     
+    ion charge -1 conc 0.000 radius 2.0    
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm mol
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# COMBINE INTO BINDING ENERGY
+print elecEnergy complex-fine - lig-fine - pka-fine end
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pka-lig/apbs-mol-surf.out

@@ -0,0 +1,271 @@
+
+
+----------------------------------------------------------------------
+    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-surf.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
+  47 atoms
+  Centered at (2.482e+01, -3.315e+01, 2.154e+01)
+  Net charge 1.11e-16 e
+Reading PQR-format atom data from bx6_7_apo_apbs.pqr.
+  3423 atoms
+  Centered at (2.897e+01, -3.251e+01, 2.702e+01)
+  Net charge 1.00e+00 e
+Reading PQR-format atom data from bx6_7_bin_apbs.pqr.
+  3470 atoms
+  Centered at (2.897e+01, -3.251e+01, 2.702e+01)
+  Net charge 1.00e+00 e
+Preparing to run 6 PBE calculations.
+----------------------------------------
+CALCULATION #1 (lig-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  203.877 MB total, 203.877 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.729 x 0.729 x 0.729
+  Grid lengths: 70.000 x 70.000 x 70.000
+  Grid center: (28.969, -32.507, 27.022)
+  Multigrid levels: 4
+  Molecule ID: 1
+  Linearized traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 2.244350164274E+03 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #2 (lig-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  203.877 MB total, 405.586 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.250 x 0.250 x 0.250
+  Grid lengths: 24.000 x 24.000 x 24.000
+  Grid center: (24.822, -33.153, 21.545)
+  Multigrid levels: 4
+  Molecule ID: 1
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.052149475373E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (pka-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  251.521 MB total, 405.586 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.729 x 0.729 x 0.729
+  Grid lengths: 70.000 x 70.000 x 70.000
+  Grid center: (28.969, -32.507, 27.022)
+  Multigrid levels: 4
+  Molecule ID: 2
+  Linearized traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.862615690066E+05 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #4 (pka-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  251.521 MB total, 493.795 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.250 x 0.250 x 0.250
+  Grid lengths: 24.000 x 24.000 x 24.000
+  Grid center: (24.822, -33.153, 21.545)
+  Multigrid levels: 4
+  Molecule ID: 2
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 3.051810884053E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #5 (complex-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  251.858 MB total, 493.795 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.729 x 0.729 x 0.729
+  Grid lengths: 70.000 x 70.000 x 70.000
+  Grid center: (28.969, -32.507, 27.022)
+  Multigrid levels: 4
+  Molecule ID: 3
+  Linearized traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.886625455219E+05 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #6 (complex-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  251.858 MB total, 494.601 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.250 x 0.250 x 0.250
+  Grid lengths: 24.000 x 24.000 x 24.000
+  Grid center: (24.822, -33.153, 21.545)
+  Multigrid levels: 4
+  Molecule ID: 3
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 1.400 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 3.158218439277E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end
+  Local net energy (PE 0) = 1.192607686581E+02 kJ/mol
+  Global net ELEC energy = 1.192607686581E+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, 494.601 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pka-lig/apbs-mol-vdw.in

@@ -0,0 +1,145 @@
+##########################################################################
+# PROTEIN KINASE BINDING ENERGY -- VAN DER WAALS SURFACE
+##########################################################################
+
+read 
+    mol pqr bx6_7_lig_apbs.pqr
+    mol pqr bx6_7_apo_apbs.pqr
+    mol pqr bx6_7_bin_apbs.pqr
+end
+
+# LIGAND ENERGY (FOCUSING)
+elec name lig-coarse
+    mg-manual
+    dime 97 97 97
+    glen 70 70 70
+    gcent mol 3
+    mol 1
+    lpbe
+    bcfl sdh
+    ion charge 1 conc 0.000 radius 2.0                 
+    ion charge -1 conc 0.000 radius 2.0              
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm mol
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+elec name lig-fine
+    mg-manual
+    dime 97 97 97
+    grid 0.25 0.25 0.25
+    gcent mol 1
+    mol 1
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.000 radius 2.0                 
+    ion charge -1 conc 0.000 radius 2.0 
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm mol
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# KINASE ENERGY (FOCUSING)
+elec name pka-coarse
+    mg-manual
+    dime 97 97 97
+    glen 70 70 70
+    gcent mol 3
+    mol 2
+    lpbe
+    bcfl sdh
+    ion charge 1 conc 0.000 radius 2.0                 
+    ion charge -1 conc 0.000 radius 2.0 
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm mol
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+elec name pka-fine
+    mg-manual
+    dime 97 97 97
+    grid 0.25 0.25 0.25
+    gcent mol 1
+    mol 2
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.000 radius 2.0                 
+    ion charge -1 conc 0.000 radius 2.0 
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm mol
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# COMPLEX ENERGY (FOCUSING)
+elec name complex-coarse
+    mg-manual
+    dime 97 97 97
+    glen 70 70 70
+    gcent mol 3
+    mol 3
+    lpbe 
+    bcfl sdh
+    ion charge 1 conc 0.000 radius 2.0                 
+    ion charge -1 conc 0.000 radius 2.0 
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm mol
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+elec name complex-fine
+    mg-manual
+    dime 97 97 97
+    grid 0.25 0.25 0.25
+    gcent mol 1
+    mol 3
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.000 radius 2.0                 
+    ion charge -1 conc 0.000 radius 2.0 
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm mol
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+print elecEnergy complex-fine - lig-fine - pka-fine end
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pka-lig/apbs-mol-vdw.out

@@ -0,0 +1,271 @@
+
+
+----------------------------------------------------------------------
+    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-vdw.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
+  47 atoms
+  Centered at (2.482e+01, -3.315e+01, 2.154e+01)
+  Net charge 1.11e-16 e
+Reading PQR-format atom data from bx6_7_apo_apbs.pqr.
+  3423 atoms
+  Centered at (2.897e+01, -3.251e+01, 2.702e+01)
+  Net charge 1.00e+00 e
+Reading PQR-format atom data from bx6_7_bin_apbs.pqr.
+  3470 atoms
+  Centered at (2.897e+01, -3.251e+01, 2.702e+01)
+  Net charge 1.00e+00 e
+Preparing to run 6 PBE calculations.
+----------------------------------------
+CALCULATION #1 (lig-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  204.292 MB total, 204.292 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.729 x 0.729 x 0.729
+  Grid lengths: 70.000 x 70.000 x 70.000
+  Grid center: (28.969, -32.507, 27.022)
+  Multigrid levels: 4
+  Molecule ID: 1
+  Linearized traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 2.224988750664E+03 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #2 (lig-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  204.292 MB total, 406.001 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.250 x 0.250 x 0.250
+  Grid lengths: 24.000 x 24.000 x 24.000
+  Grid center: (24.822, -33.153, 21.545)
+  Multigrid levels: 4
+  Molecule ID: 1
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.049695084686E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (pka-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  291.151 MB total, 406.001 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.729 x 0.729 x 0.729
+  Grid lengths: 70.000 x 70.000 x 70.000
+  Grid center: (28.969, -32.507, 27.022)
+  Multigrid levels: 4
+  Molecule ID: 2
+  Linearized traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.818450789522E+05 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #4 (pka-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  291.151 MB total, 533.426 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.250 x 0.250 x 0.250
+  Grid lengths: 24.000 x 24.000 x 24.000
+  Grid center: (24.822, -33.153, 21.545)
+  Multigrid levels: 4
+  Molecule ID: 2
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 3.008254338259E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #5 (complex-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  292.063 MB total, 533.426 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.729 x 0.729 x 0.729
+  Grid lengths: 70.000 x 70.000 x 70.000
+  Grid center: (28.969, -32.507, 27.022)
+  Multigrid levels: 4
+  Molecule ID: 3
+  Linearized traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.840918409896E+05 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #6 (complex-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  292.063 MB total, 534.806 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.250 x 0.250 x 0.250
+  Grid lengths: 24.000 x 24.000 x 24.000
+  Grid center: (24.822, -33.153, 21.545)
+  Multigrid levels: 4
+  Molecule ID: 3
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition; no smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 3.113304681884E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end
+  Local net energy (PE 0) = 8.083515648730E+00 kJ/mol
+  Global net ELEC energy = 8.083515648730E+00 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, 534.806 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pka-lig/apbs-smol-surf.in

@@ -0,0 +1,146 @@
+##########################################################################
+# PROTEIN KINASE INHIBITOR BINDING ENERGY -- MOLECULAR SURFACE
+##########################################################################
+
+read 
+    mol pqr bx6_7_lig_apbs.pqr
+    mol pqr bx6_7_apo_apbs.pqr
+    mol pqr bx6_7_bin_apbs.pqr
+end
+
+# LIGAND ENERGY (FOCUSING)
+elec name lig-coarse
+    mg-manual
+    dime 97 97 97 
+    glen 70 70 70
+    gcent mol 3
+    mol 1
+    lpbe
+    bcfl sdh
+    ion charge 1 conc 0.000 radius 2.0     
+    ion charge -1 conc 0.000 radius 2.0      
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm smol
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+elec name lig-fine
+    mg-manual
+    dime 97 97 97
+    grid 0.25 0.25 0.25
+    gcent mol 1
+    mol 1
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.000 radius 2.0     
+    ion charge -1 conc 0.000 radius 2.0        
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm smol
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# KINASE ENERGY (FOCUSING)
+elec name pka-coarse
+    mg-manual
+    dime 97 97 97
+    glen 70 70 70
+    gcent mol 3
+    mol 2
+    lpbe
+    bcfl sdh
+    ion charge 1 conc 0.000 radius 2.0     
+    ion charge -1 conc 0.000 radius 2.0    
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm smol
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+elec name pka-fine
+    mg-manual
+    dime 97 97 97
+    grid 0.25 0.25 0.25
+    gcent mol 1
+    mol 2
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.000 radius 2.0     
+    ion charge -1 conc 0.000 radius 2.0    
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm smol
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# COMPLEX ENERGY (FOCUSING)
+elec name complex-coarse
+    mg-manual
+    dime 97 97 97
+    glen 70 70 70
+    gcent mol 3
+    mol 3
+    lpbe
+    bcfl sdh
+    ion charge 1 conc 0.000 radius 2.0
+    ion charge -1 conc 0.000 radius 2.0
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm smol
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+elec name complex-fine
+    mg-manual
+    dime 97 97 97
+    grid 0.25 0.25 0.25
+    gcent mol 1
+    mol 3
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.000 radius 2.0     
+    ion charge -1 conc 0.000 radius 2.0    
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm smol
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# COMBINE INTO BINDING ENERGY
+print elecEnergy complex-fine - lig-fine - pka-fine end
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pka-lig/apbs-smol-surf.out

@@ -0,0 +1,271 @@
+
+
+----------------------------------------------------------------------
+    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-surf.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
+  47 atoms
+  Centered at (2.482e+01, -3.315e+01, 2.154e+01)
+  Net charge 1.11e-16 e
+Reading PQR-format atom data from bx6_7_apo_apbs.pqr.
+  3423 atoms
+  Centered at (2.897e+01, -3.251e+01, 2.702e+01)
+  Net charge 1.00e+00 e
+Reading PQR-format atom data from bx6_7_bin_apbs.pqr.
+  3470 atoms
+  Centered at (2.897e+01, -3.251e+01, 2.702e+01)
+  Net charge 1.00e+00 e
+Preparing to run 6 PBE calculations.
+----------------------------------------
+CALCULATION #1 (lig-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  203.877 MB total, 203.877 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.729 x 0.729 x 0.729
+  Grid lengths: 70.000 x 70.000 x 70.000
+  Grid center: (28.969, -32.507, 27.022)
+  Multigrid levels: 4
+  Molecule ID: 1
+  Linearized traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  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 = 2.251466789420E+03 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #2 (lig-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  203.877 MB total, 405.586 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.250 x 0.250 x 0.250
+  Grid lengths: 24.000 x 24.000 x 24.000
+  Grid center: (24.822, -33.153, 21.545)
+  Multigrid levels: 4
+  Molecule ID: 1
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  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 = 1.052814502873E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (pka-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  251.521 MB total, 405.586 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.729 x 0.729 x 0.729
+  Grid lengths: 70.000 x 70.000 x 70.000
+  Grid center: (28.969, -32.507, 27.022)
+  Multigrid levels: 4
+  Molecule ID: 2
+  Linearized traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  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 = 1.864071689626E+05 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #4 (pka-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  251.521 MB total, 493.795 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.250 x 0.250 x 0.250
+  Grid lengths: 24.000 x 24.000 x 24.000
+  Grid center: (24.822, -33.153, 21.545)
+  Multigrid levels: 4
+  Molecule ID: 2
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  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 = 3.053319953673E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #5 (complex-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  251.858 MB total, 493.795 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.729 x 0.729 x 0.729
+  Grid lengths: 70.000 x 70.000 x 70.000
+  Grid center: (28.969, -32.507, 27.022)
+  Multigrid levels: 4
+  Molecule ID: 3
+  Linearized traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  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 = 1.888027142979E+05 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #6 (complex-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  251.858 MB total, 494.601 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.250 x 0.250 x 0.250
+  Grid lengths: 24.000 x 24.000 x 24.000
+  Grid center: (24.822, -33.153, 21.545)
+  Multigrid levels: 4
+  Molecule ID: 3
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  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 = 3.159690177241E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end
+  Local net energy (PE 0) = 1.088773280806E+02 kJ/mol
+  Global net ELEC energy = 1.088773280806E+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, 494.601 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pka-lig/apbs-smol-vdw.in

@@ -0,0 +1,145 @@
+##########################################################################
+# PROTEIN KINASE BINDING ENERGY -- VAN DER WAALS SURFACE
+##########################################################################
+
+read 
+    mol pqr bx6_7_lig_apbs.pqr
+    mol pqr bx6_7_apo_apbs.pqr
+    mol pqr bx6_7_bin_apbs.pqr
+end
+
+# LIGAND ENERGY (FOCUSING)
+elec name lig-coarse
+    mg-manual
+    dime 97 97 97
+    glen 70 70 70
+    gcent mol 3
+    mol 1
+    lpbe
+    bcfl sdh
+    ion charge 1 conc 0.000 radius 2.0                 
+    ion charge -1 conc 0.000 radius 2.0              
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm smol
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+elec name lig-fine
+    mg-manual
+    dime 97 97 97
+    grid 0.25 0.25 0.25
+    gcent mol 1
+    mol 1
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.000 radius 2.0                 
+    ion charge -1 conc 0.000 radius 2.0 
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm smol
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# KINASE ENERGY (FOCUSING)
+elec name pka-coarse
+    mg-manual
+    dime 97 97 97
+    glen 70 70 70
+    gcent mol 3
+    mol 2
+    lpbe
+    bcfl sdh
+    ion charge 1 conc 0.000 radius 2.0                 
+    ion charge -1 conc 0.000 radius 2.0 
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm smol
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+elec name pka-fine
+    mg-manual
+    dime 97 97 97
+    grid 0.25 0.25 0.25
+    gcent mol 1
+    mol 2
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.000 radius 2.0                 
+    ion charge -1 conc 0.000 radius 2.0 
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm smol
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+# COMPLEX ENERGY (FOCUSING)
+elec name complex-coarse
+    mg-manual
+    dime 97 97 97
+    glen 70 70 70
+    gcent mol 3
+    mol 3
+    lpbe 
+    bcfl sdh
+    ion charge 1 conc 0.000 radius 2.0                 
+    ion charge -1 conc 0.000 radius 2.0 
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm smol
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+elec name complex-fine
+    mg-manual
+    dime 97 97 97
+    grid 0.25 0.25 0.25
+    gcent mol 1
+    mol 3
+    lpbe
+    bcfl focus
+    ion charge 1 conc 0.000 radius 2.0                 
+    ion charge -1 conc 0.000 radius 2.0 
+    pdie 2.0
+    sdie 78.00
+    chgm spl0
+    srfm smol
+    srad 0.0
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy total
+    calcforce no
+end
+
+print elecEnergy complex-fine - lig-fine - pka-fine end
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pka-lig/apbs-smol-vdw.out

@@ -0,0 +1,271 @@
+
+
+----------------------------------------------------------------------
+    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-vdw.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
+  47 atoms
+  Centered at (2.482e+01, -3.315e+01, 2.154e+01)
+  Net charge 1.11e-16 e
+Reading PQR-format atom data from bx6_7_apo_apbs.pqr.
+  3423 atoms
+  Centered at (2.897e+01, -3.251e+01, 2.702e+01)
+  Net charge 1.00e+00 e
+Reading PQR-format atom data from bx6_7_bin_apbs.pqr.
+  3470 atoms
+  Centered at (2.897e+01, -3.251e+01, 2.702e+01)
+  Net charge 1.00e+00 e
+Preparing to run 6 PBE calculations.
+----------------------------------------
+CALCULATION #1 (lig-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  204.292 MB total, 204.292 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.729 x 0.729 x 0.729
+  Grid lengths: 70.000 x 70.000 x 70.000
+  Grid center: (28.969, -32.507, 27.022)
+  Multigrid levels: 4
+  Molecule ID: 1
+  Linearized traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 2.226793167046E+03 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #2 (lig-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  204.292 MB total, 406.001 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.250 x 0.250 x 0.250
+  Grid lengths: 24.000 x 24.000 x 24.000
+  Grid center: (24.822, -33.153, 21.545)
+  Multigrid levels: 4
+  Molecule ID: 1
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.050504485887E+04 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (pka-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  291.151 MB total, 406.001 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.729 x 0.729 x 0.729
+  Grid lengths: 70.000 x 70.000 x 70.000
+  Grid center: (28.969, -32.507, 27.022)
+  Multigrid levels: 4
+  Molecule ID: 2
+  Linearized traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.827976621645E+05 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #4 (pka-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  291.151 MB total, 533.426 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.250 x 0.250 x 0.250
+  Grid lengths: 24.000 x 24.000 x 24.000
+  Grid center: (24.822, -33.153, 21.545)
+  Multigrid levels: 4
+  Molecule ID: 2
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 3.017228546773E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #5 (complex-coarse): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  292.063 MB total, 533.426 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.729 x 0.729 x 0.729
+  Grid lengths: 70.000 x 70.000 x 70.000
+  Grid center: (28.969, -32.507, 27.022)
+  Multigrid levels: 4
+  Molecule ID: 3
+  Linearized traditional PBE
+  Single Debye-Huckel sphere boundary conditions
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.850819075387E+05 kJ/mol
+  Calculating forces...
+[focusFillBound()]: WARNING:
+    Unusually large potential values
+    detected on the focusing boundary!
+    Convergence not guaranteed for NPBE/NRPBE calculations!
+
+----------------------------------------
+CALCULATION #6 (complex-fine): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  292.063 MB total, 534.806 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 97 x 97 x 97
+  Grid spacings: 0.250 x 0.250 x 0.250
+  Grid lengths: 24.000 x 24.000 x 24.000
+  Grid center: (24.822, -33.153, 21.545)
+  Multigrid levels: 4
+  Molecule ID: 3
+  Linearized traditional PBE
+  Boundary conditions from focusing
+  2 ion species (0.000 M ionic strength):
+    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
+    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
+  Solute dielectric: 2.000
+  Solvent dielectric: 78.000
+  Using "molecular" surface definition;harmonic average smoothing
+  Solvent probe radius: 0.000 A
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 3.122488625388E+05 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end
+  Local net energy (PE 0) = 2.096300255723E+01 kJ/mol
+  Global net ELEC energy = 2.096300255723E+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, 534.806 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/pka-lig/bx6_7_lig_apbs.pqr

@@ -0,0 +1,47 @@
+ATOM   3424  C1  BX6   351      22.758 -32.646  24.883  0.550 1.870
+ATOM   3425  C8  BX6   351      21.510 -33.006  25.576  0.000 2.040
+ATOM   3426  C9  BX6   351      21.396 -34.314  26.095  0.000 1.990
+ATOM   3427  C10 BX6   351      20.219 -34.702  26.754  0.000 1.990
+ATOM   3428  C11 BX6   351      19.169 -33.770  26.877  0.250 2.040
+ATOM   3429  O1  BX6   351      17.998 -34.158  27.496 -0.650 1.550
+ATOM   3430  C12 BX6   351      19.279 -32.456  26.383  0.000 1.990
+ATOM   3431  C13 BX6   351      20.457 -32.073  25.721  0.000 1.990
+ATOM   3432  O2  BX6   351      23.656 -33.453  24.670 -0.550 1.550
+ATOM   3433  N2  BX6   351      22.872 -31.357  24.491 -0.350 1.830
+ATOM   3434  N1  BX6   351      26.155 -29.614  24.198 -0.300 1.650
+ATOM   3435  C2  BX6   351      24.835 -29.952  24.746  0.300 2.235
+ATOM   3436  C3  BX6   351      24.113 -30.950  23.837  0.100 2.265
+ATOM   3437  C4  BX6   351      23.795 -30.459  22.416  0.250 2.265
+ATOM   3438  C5  BX6   351      23.954 -28.951  22.169  0.000 2.235
+ATOM   3439  C6  BX6   351      25.401 -28.443  22.138  0.000 2.235
+ATOM   3440  C7  BX6   351      26.083 -28.320  23.505  0.300 2.235
+ATOM   3441  O3  BX6   351      24.606 -31.211  21.456 -0.550 1.600
+ATOM   3442  C14 BX6   351      24.157 -31.482  20.238  0.700 1.870
+ATOM   3443  O4  BX6   351      23.102 -31.107  19.824 -0.400 1.520
+ATOM   3444  C15 BX6   351      25.053 -32.334  19.447  0.000 2.040
+ATOM   3445  C16 BX6   351      24.584 -32.927  18.272  0.000 1.990
+ATOM   3446  C17 BX6   351      25.397 -33.802  17.546  0.250 2.040
+ATOM   3447  O5  BX6   351      24.862 -34.331  16.386 -0.650 1.550
+ATOM   3448  C18 BX6   351      26.691 -34.119  18.005  0.000 2.040
+ATOM   3449  C19 BX6   351      27.171 -33.490  19.175  0.250 2.040
+ATOM   3450  O6  BX6   351      28.416 -33.747  19.715 -0.650 1.550
+ATOM   3451  C20 BX6   351      26.362 -32.582  19.867  0.000 1.990
+ATOM   3452  C21 BX6   351      27.475 -35.140  17.267  0.400 1.870
+ATOM   3453  O7  BX6   351      26.946 -35.882  16.448 -0.400 1.550
+ATOM   3454  C22 BX6   351      28.916 -35.270  17.535  0.000 2.040
+ATOM   3455  C23 BX6   351      29.344 -36.371  18.289  0.250 2.040
+ATOM   3456  O8  BX6   351      28.427 -37.285  18.770 -0.650 1.550
+ATOM   3457  C24 BX6   351      30.703 -36.559  18.569  0.000 1.990
+ATOM   3458  C25 BX6   351      31.646 -35.633  18.114  0.000 1.990
+ATOM   3459  C26 BX6   351      31.224 -34.528  17.366  0.000 1.990
+ATOM   3460  C27 BX6   351      29.864 -34.340  17.054  0.000 2.040
+ATOM   3461  C28 BX6   351      29.480 -33.190  16.214  0.140 1.870
+ATOM   3462  O9  BX6   351      30.052 -32.107  16.355 -0.570 1.660
+ATOM   3463  O10 BX6   351      28.595 -33.344  15.376 -0.570 1.660
+ATOM   3464  H1  BX6   351      18.044 -35.081  27.714  0.400 0.760
+ATOM   3465  H2  BX6   351      22.142 -30.695  24.663  0.250 0.800
+ATOM   3466  H3  BX6   351      26.483 -30.339  23.572  0.350 0.800
+ATOM   3467  H4  BX6   351      25.537 -34.741  15.864  0.400 0.760
+ATOM   3468  H5  BX6   351      28.438 -33.485  20.628  0.400 0.760
+ATOM   3469  H6  BX6   351      28.878 -37.986  19.224  0.400 0.760
+ATOM   3470  H7  BX6   351      26.819 -29.545  24.959  0.350 0.800

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

@@ -0,0 +1,36 @@
+README for point-pmf APBS examples
+==================================
+
+The example input files in this directory see how well we do reproducing Coulomb's law.
+
+Be sure to edit the runme.sh script to point to the APBS binary.
+
+This example was contributed by Nathan Baker.
+
+Input File|Description|APBS Version|Results (kJ/mol)||||Analytical (kJ/mol)||||
+---|---|---|---|---|---|---|---|---|---|---
+||||1 A Dist|2 A Dist|3 A Dist|4 A Dist|1 A Dist|2 A Dist|3 A Dist|4 A Dist
+[apbs.in](apbs.in)|Focusing to 0.21 A, srfm spl2|**1.5**|**18.3082**|**8.90669**|**5.9096**|**4.43014**|17.686|8.843|5.89533|4.4215
+|||1.4.2|18.3082|8.90669|5.9096|4.43014
+|||1.4.1|18.3082|8.9067|5.9096|4.4301
+|||1.4|18.3082|8.9067|5.9096|4.4301
+|||1.3|18.3082|8.9067|5.9096|4.4301
+|||1.2.1|18.3082|8.9067|5.9096|4.4301
+|||1.2|18.3082|8.9067|5.9096|4.4301
+|||1.1.0|18.3082|8.9067|5.9096|4.4301
+|||1.0.0|18.3082|8.9067|5.9096|4.4301
+|||0.5.1|18.3082|8.9067|5.9096|4.4301
+|||0.5.0|18.3082|8.9067|5.9096|4.4301
+|||0.4.0|18.3082|8.9067|5.9096|4.4301
+|||0.3.2|18.3082|8.9067|5.9096|4.4301
+|||0.3.1|18.3082|8.9067|5.9096|4.4301
+|||0.3.0|18.3082|8.9067|5.9096|4.4301
+|||0.2.6|18.3082|8.9067|5.9096|4.4301
+|||0.2.5|18.3082|8.9067|5.9096|4.4301
+|||0.2.4|18.3082|8.9067|5.9096|4.4301
+|||0.2.3|18.3082|8.9067|5.9096|4.4301
+|||0.2.2|18.3082|8.9067|5.9096|4.4301
+|||0.2.1|18.308|8.907|5.910|4.430
+|||0.2.0|18.31|8.91|5.91|4.43
+|||0.1.8|18.308|8.907|5.910|4.430
+

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

@@ -0,0 +1,78 @@
+##########################################################################
+# POINT CHARGE POTENTIAL OF MEAN FORCE
+##########################################################################
+
+read 
+    mol pqr mol1.pqr
+    mol pqr mol2.pqr
+    mol pqr complex.pqr
+end
+
+# COMPONENT 1 ENERGY
+elec name point1
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 1
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no 
+end
+
+# COMPONENT 2 ENERGY
+elec name point2
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 2
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no
+end
+
+# COMPLEX ENERGY 
+elec name complex
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 3
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no
+end
+
+# BINDING ENERGY
+print elecEnergy complex - point1 - point2 end
+
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/complex-0_1.in

@@ -0,0 +1,78 @@
+##########################################################################
+# POINT CHARGE POTENTIAL OF MEAN FORCE
+##########################################################################
+
+read 
+    mol pqr mol0.pqr
+    mol pqr mol1.pqr
+    mol pqr complex-0_1.pqr
+end
+
+# COMPONENT 1 ENERGY
+elec name point1
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 1
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no 
+end
+
+# COMPONENT 2 ENERGY
+elec name point2
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 2
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no
+end
+
+# COMPLEX ENERGY 
+elec name complex
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 3
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no
+end
+
+# BINDING ENERGY
+print elecEnergy complex - point1 - point2 end
+
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/complex-0_1.out

@@ -0,0 +1,190 @@
+
+
+----------------------------------------------------------------------
+    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 complex-0_1.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from mol0.pqr.
+  1 atoms
+  Centered at (-3.000e+00, 0.000e+00, 0.000e+00)
+  Net charge 1.00e+00 e
+Reading PQR-format atom data from mol1.pqr.
+  1 atoms
+  Centered at (-2.000e+00, 0.000e+00, 0.000e+00)
+  Net charge 1.00e+00 e
+Reading PQR-format atom data from complex-0_1.pqr.
+  2 atoms
+  Centered at (-2.500e+00, 0.000e+00, 0.000e+00)
+  Net charge 2.00e+00 e
+Preparing to run 3 PBE calculations.
+----------------------------------------
+CALCULATION #1 (point1): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  61.060 MB total, 61.060 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.210 x 0.210 x 0.210
+  Grid lengths: 13.440 x 13.440 x 13.440
+  Grid center: (0.000, 0.000, 0.000)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  0 ion species (0.000 M ionic strength):
+  Solute dielectric: 78.540
+  Solvent dielectric: 78.540
+  Using spline-based surface definition;window = 0.300
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 9.776035707281E+01 kJ/mol
+  Fixed charge energy = 97.7604 kJ/mol
+  Mobile charge energy = 0 kJ/mol
+  Dielectric energy = 96.5336 kJ/mol
+  Per-atom energies:
+      Atom 0:  9.776035707281E+01 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #2 (point2): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  61.060 MB total, 61.067 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.210 x 0.210 x 0.210
+  Grid lengths: 13.440 x 13.440 x 13.440
+  Grid center: (0.000, 0.000, 0.000)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  0 ion species (0.000 M ionic strength):
+  Solute dielectric: 78.540
+  Solvent dielectric: 78.540
+  Using spline-based surface definition;window = 0.300
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 8.975920687031E+01 kJ/mol
+  Fixed charge energy = 89.7592 kJ/mol
+  Mobile charge energy = 0 kJ/mol
+  Dielectric energy = 88.6151 kJ/mol
+  Per-atom energies:
+      Atom 0:  8.975920687031E+01 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (complex): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  61.060 MB total, 61.067 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.210 x 0.210 x 0.210
+  Grid lengths: 13.440 x 13.440 x 13.440
+  Grid center: (0.000, 0.000, 0.000)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  0 ion species (0.000 M ionic strength):
+  Solute dielectric: 78.540
+  Solvent dielectric: 78.540
+  Using spline-based surface definition;window = 0.300
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 2.058277719334E+02 kJ/mol
+  Fixed charge energy = 205.828 kJ/mol
+  Mobile charge energy = 0 kJ/mol
+  Dielectric energy = 201.106 kJ/mol
+  Per-atom energies:
+      Atom 0:  1.069144350786E+02 kJ/mol
+      Atom 1:  9.891333685475E+01 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 3 (complex) - 1 (point1) - 2 (point2) end
+  Local net energy (PE 0) = 1.830820799027E+01 kJ/mol
+  Global net ELEC energy = 1.830820799027E+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, 61.067 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/complex-0_1.pqr

@@ -0,0 +1,2 @@
+ATOM      1  I   ION     1      -3.000    0.000   0.000  1.00 0.00
+ATOM      1  I   ION     1      -2.000    0.000   0.000  1.00 0.00

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/complex-0_2.in

@@ -0,0 +1,78 @@
+##########################################################################
+# POINT CHARGE POTENTIAL OF MEAN FORCE
+##########################################################################
+
+read 
+    mol pqr mol0.pqr
+    mol pqr mol2.pqr
+    mol pqr complex-0_2.pqr
+end
+
+# COMPONENT 1 ENERGY
+elec name point1
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 1
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no 
+end
+
+# COMPONENT 2 ENERGY
+elec name point2
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 2
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no
+end
+
+# COMPLEX ENERGY 
+elec name complex
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 3
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no
+end
+
+# BINDING ENERGY
+print elecEnergy complex - point1 - point2 end
+
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/complex-0_2.out

@@ -0,0 +1,190 @@
+
+
+----------------------------------------------------------------------
+    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 complex-0_2.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from mol0.pqr.
+  1 atoms
+  Centered at (-3.000e+00, 0.000e+00, 0.000e+00)
+  Net charge 1.00e+00 e
+Reading PQR-format atom data from mol2.pqr.
+  1 atoms
+  Centered at (-1.000e+00, 0.000e+00, 0.000e+00)
+  Net charge 1.00e+00 e
+Reading PQR-format atom data from complex-0_2.pqr.
+  2 atoms
+  Centered at (-2.000e+00, 0.000e+00, 0.000e+00)
+  Net charge 2.00e+00 e
+Preparing to run 3 PBE calculations.
+----------------------------------------
+CALCULATION #1 (point1): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  61.060 MB total, 61.060 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.210 x 0.210 x 0.210
+  Grid lengths: 13.440 x 13.440 x 13.440
+  Grid center: (0.000, 0.000, 0.000)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  0 ion species (0.000 M ionic strength):
+  Solute dielectric: 78.540
+  Solvent dielectric: 78.540
+  Using spline-based surface definition;window = 0.300
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 9.776035707281E+01 kJ/mol
+  Fixed charge energy = 97.7604 kJ/mol
+  Mobile charge energy = 0 kJ/mol
+  Dielectric energy = 96.5336 kJ/mol
+  Per-atom energies:
+      Atom 0:  9.776035707281E+01 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #2 (point2): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  61.060 MB total, 61.067 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.210 x 0.210 x 0.210
+  Grid lengths: 13.440 x 13.440 x 13.440
+  Grid center: (0.000, 0.000, 0.000)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  0 ion species (0.000 M ionic strength):
+  Solute dielectric: 78.540
+  Solvent dielectric: 78.540
+  Using spline-based surface definition;window = 0.300
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.017611498797E+02 kJ/mol
+  Fixed charge energy = 101.761 kJ/mol
+  Mobile charge energy = 0 kJ/mol
+  Dielectric energy = 100.656 kJ/mol
+  Per-atom energies:
+      Atom 0:  1.017611498797E+02 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (complex): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  61.060 MB total, 61.068 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.210 x 0.210 x 0.210
+  Grid lengths: 13.440 x 13.440 x 13.440
+  Grid center: (0.000, 0.000, 0.000)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  0 ion species (0.000 M ionic strength):
+  Solute dielectric: 78.540
+  Solvent dielectric: 78.540
+  Using spline-based surface definition;window = 0.300
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 2.084282010393E+02 kJ/mol
+  Fixed charge energy = 208.428 kJ/mol
+  Mobile charge energy = 0 kJ/mol
+  Dielectric energy = 203.83 kJ/mol
+  Per-atom energies:
+      Atom 0:  1.022136878480E+02 kJ/mol
+      Atom 1:  1.062145131913E+02 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 3 (complex) - 1 (point1) - 2 (point2) end
+  Local net energy (PE 0) = 8.906694086750E+00 kJ/mol
+  Global net ELEC energy = 8.906694086750E+00 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, 61.068 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/complex-0_2.pqr

@@ -0,0 +1,2 @@
+ATOM      1  I   ION     1      -3.000    0.000   0.000  1.00 0.00
+ATOM      1  I   ION     1      -1.000    0.000   0.000  1.00 0.00

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/complex-0_3.in

@@ -0,0 +1,78 @@
+##########################################################################
+# POINT CHARGE POTENTIAL OF MEAN FORCE
+##########################################################################
+
+read 
+    mol pqr mol0.pqr
+    mol pqr mol3.pqr
+    mol pqr complex-0_3.pqr
+end
+
+# COMPONENT 1 ENERGY
+elec name point1
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 1
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no 
+end
+
+# COMPONENT 2 ENERGY
+elec name point2
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 2
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no
+end
+
+# COMPLEX ENERGY 
+elec name complex
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 3
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no
+end
+
+# BINDING ENERGY
+print elecEnergy complex - point1 - point2 end
+
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/complex-0_3.out

@@ -0,0 +1,190 @@
+
+
+----------------------------------------------------------------------
+    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 complex-0_3.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from mol0.pqr.
+  1 atoms
+  Centered at (-3.000e+00, 0.000e+00, 0.000e+00)
+  Net charge 1.00e+00 e
+Reading PQR-format atom data from mol3.pqr.
+  1 atoms
+  Centered at (0.000e+00, 0.000e+00, 0.000e+00)
+  Net charge 1.00e+00 e
+Reading PQR-format atom data from complex-0_3.pqr.
+  2 atoms
+  Centered at (-1.500e+00, 0.000e+00, 0.000e+00)
+  Net charge 2.00e+00 e
+Preparing to run 3 PBE calculations.
+----------------------------------------
+CALCULATION #1 (point1): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  61.060 MB total, 61.060 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.210 x 0.210 x 0.210
+  Grid lengths: 13.440 x 13.440 x 13.440
+  Grid center: (0.000, 0.000, 0.000)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  0 ion species (0.000 M ionic strength):
+  Solute dielectric: 78.540
+  Solvent dielectric: 78.540
+  Using spline-based surface definition;window = 0.300
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 9.776035707281E+01 kJ/mol
+  Fixed charge energy = 97.7604 kJ/mol
+  Mobile charge energy = 0 kJ/mol
+  Dielectric energy = 96.5336 kJ/mol
+  Per-atom energies:
+      Atom 0:  9.776035707281E+01 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #2 (point2): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  61.060 MB total, 61.067 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.210 x 0.210 x 0.210
+  Grid lengths: 13.440 x 13.440 x 13.440
+  Grid center: (0.000, 0.000, 0.000)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  0 ion species (0.000 M ionic strength):
+  Solute dielectric: 78.540
+  Solvent dielectric: 78.540
+  Using spline-based surface definition;window = 0.300
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.337661883222E+02 kJ/mol
+  Fixed charge energy = 133.766 kJ/mol
+  Mobile charge energy = 0 kJ/mol
+  Dielectric energy = 132.672 kJ/mol
+  Per-atom energies:
+      Atom 0:  1.337661883222E+02 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (complex): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  61.060 MB total, 61.068 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.210 x 0.210 x 0.210
+  Grid lengths: 13.440 x 13.440 x 13.440
+  Grid center: (0.000, 0.000, 0.000)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  0 ion species (0.000 M ionic strength):
+  Solute dielectric: 78.540
+  Solvent dielectric: 78.540
+  Using spline-based surface definition;window = 0.300
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 2.374361452120E+02 kJ/mol
+  Fixed charge energy = 237.436 kJ/mol
+  Mobile charge energy = 0 kJ/mol
+  Dielectric energy = 232.924 kJ/mol
+  Per-atom energies:
+      Atom 0:  1.007151570480E+02 kJ/mol
+      Atom 1:  1.367209881640E+02 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 3 (complex) - 1 (point1) - 2 (point2) end
+  Local net energy (PE 0) = 5.909599816984E+00 kJ/mol
+  Global net ELEC energy = 5.909599816984E+00 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, 61.068 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/complex-0_3.pqr

@@ -0,0 +1,2 @@
+ATOM      1  I   ION     1      -3.000    0.000   0.000  1.00 0.00
+ATOM      1  I   ION     1       0.000    0.000   0.000  1.00 0.00

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/complex-0_4.in

@@ -0,0 +1,78 @@
+##########################################################################
+# POINT CHARGE POTENTIAL OF MEAN FORCE
+##########################################################################
+
+read 
+    mol pqr mol0.pqr
+    mol pqr mol4.pqr
+    mol pqr complex-0_4.pqr
+end
+
+# COMPONENT 1 ENERGY
+elec name point1
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 1
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no 
+end
+
+# COMPONENT 2 ENERGY
+elec name point2
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 2
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no
+end
+
+# COMPLEX ENERGY 
+elec name complex
+    mg-manual
+    dime 65 65 65
+    grid 0.21 0.21 0.21
+    gcent 0.0 0.0 0.0
+    mol 3
+    lpbe
+    bcfl mdh
+    pdie 78.54
+    sdie 78.54
+    chgm spl0
+    srfm spl2
+    srad 1.4
+    swin 0.3
+    sdens 10.0
+    temp 298.15
+    calcenergy comps
+    calcforce no
+end
+
+# BINDING ENERGY
+print elecEnergy complex - point1 - point2 end
+
+
+quit

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/complex-0_4.out

@@ -0,0 +1,190 @@
+
+
+----------------------------------------------------------------------
+    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 complex-0_4.in...
+rank 0 size 1...
+Parsed input file.
+Got paths for 3 molecules
+Reading PQR-format atom data from mol0.pqr.
+  1 atoms
+  Centered at (-3.000e+00, 0.000e+00, 0.000e+00)
+  Net charge 1.00e+00 e
+Reading PQR-format atom data from mol4.pqr.
+  1 atoms
+  Centered at (1.000e+00, 0.000e+00, 0.000e+00)
+  Net charge 1.00e+00 e
+Reading PQR-format atom data from complex-0_4.pqr.
+  2 atoms
+  Centered at (-1.000e+00, 0.000e+00, 0.000e+00)
+  Net charge 2.00e+00 e
+Preparing to run 3 PBE calculations.
+----------------------------------------
+CALCULATION #1 (point1): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  61.060 MB total, 61.060 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.210 x 0.210 x 0.210
+  Grid lengths: 13.440 x 13.440 x 13.440
+  Grid center: (0.000, 0.000, 0.000)
+  Multigrid levels: 5
+  Molecule ID: 1
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  0 ion species (0.000 M ionic strength):
+  Solute dielectric: 78.540
+  Solvent dielectric: 78.540
+  Using spline-based surface definition;window = 0.300
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 9.776035707281E+01 kJ/mol
+  Fixed charge energy = 97.7604 kJ/mol
+  Mobile charge energy = 0 kJ/mol
+  Dielectric energy = 96.5336 kJ/mol
+  Per-atom energies:
+      Atom 0:  9.776035707281E+01 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #2 (point2): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  61.060 MB total, 61.067 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.210 x 0.210 x 0.210
+  Grid lengths: 13.440 x 13.440 x 13.440
+  Grid center: (0.000, 0.000, 0.000)
+  Multigrid levels: 5
+  Molecule ID: 2
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  0 ion species (0.000 M ionic strength):
+  Solute dielectric: 78.540
+  Solvent dielectric: 78.540
+  Using spline-based surface definition;window = 0.300
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 1.017611498797E+02 kJ/mol
+  Fixed charge energy = 101.761 kJ/mol
+  Mobile charge energy = 0 kJ/mol
+  Dielectric energy = 100.654 kJ/mol
+  Per-atom energies:
+      Atom 0:  1.017611498797E+02 kJ/mol
+  Calculating forces...
+----------------------------------------
+CALCULATION #3 (complex): MULTIGRID
+  Setting up problem...
+  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
+  Debye length:  0 A
+  Current memory usage:  61.061 MB total, 61.068 MB high water
+  Using linear spline charge discretization.
+  Grid dimensions: 65 x 65 x 65
+  Grid spacings: 0.210 x 0.210 x 0.210
+  Grid lengths: 13.440 x 13.440 x 13.440
+  Grid center: (0.000, 0.000, 0.000)
+  Multigrid levels: 5
+  Molecule ID: 3
+  Linearized traditional PBE
+  Multiple Debye-Huckel sphere boundary conditions
+  0 ion species (0.000 M ionic strength):
+  Solute dielectric: 78.540
+  Solvent dielectric: 78.540
+  Using spline-based surface definition;window = 0.300
+  Temperature:  298.150 K
+  Electrostatic energies will be calculated
+  Total electrostatic energy = 2.039516519000E+02 kJ/mol
+  Fixed charge energy = 203.952 kJ/mol
+  Mobile charge energy = 0 kJ/mol
+  Dielectric energy = 199.493 kJ/mol
+  Per-atom energies:
+      Atom 0:  9.997541697022E+01 kJ/mol
+      Atom 1:  1.039762349297E+02 kJ/mol
+  Calculating forces...
+----------------------------------------
+PRINT STATEMENTS
+
+print energy 3 (complex) - 1 (point1) - 2 (point2) end
+  Local net energy (PE 0) = 4.430144947418E+00 kJ/mol
+  Global net ELEC energy = 4.430144947418E+00 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, 61.068 MB high water
+
+
+Thanks for using APBS!
+

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/complex-0_4.pqr

@@ -0,0 +1,2 @@
+ATOM      1  I   ION     1      -3.000    0.000   0.000  1.00 0.00
+ATOM      1  I   ION     1       1.000    0.000   0.000  1.00 0.00

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/energy.dat

@@ -0,0 +1,24 @@
+-2.75     70.744     91.2918    29.0453
+-2.50     35.372     39.4461    11.5179
+-2.25     23.5813    25.0338    6.15954
+-2.00     17.686     18.3082    3.51804
+-1.75     14.1488    14.4467    -2.10548
+-1.50     11.7907    11.9345    -1.21961
+-1.25     10.1063    10.1816    -0.74508
+-1.00     8.843      8.90669    -0.720231
+-0.75     7.86044    7.91018    -0.632789
+-0.50     7.0744     7.11074    -0.513683
+-0.25     6.43127    6.45573    -0.380329
+0.00      5.89533    5.9096     -0.242056
+0.25      5.44185    5.4566     -0.271048
+0.50      5.05314    5.06661    -0.266567
+0.75      4.71627    4.72754    -0.23896
+1.00      4.4215     4.43014    -0.195409
+1.25      4.16141    4.1673     -0.141539
+1.50      3.93022    3.93586    -0.143503
+1.75      3.72337    3.72896    -0.150133
+2.00      3.5372     3.54224    -0.142486
+2.25      3.36876    3.37295    -0.124378
+2.50      3.21564    3.21878    -0.0976477
+2.75      3.07583    3.0786     -0.090057
+3.00      2.94767    2.95056    -0.0980435

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/io.mc

@@ -0,0 +1,1680 @@
+##############################################################################
+# MC-shell I/O capture file.
+# Creation Date and Time:  Fri Apr 29 19:48:48 2022
+
+##############################################################################
+Hello world from PE 0
+Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..
+NOsh_parseInput:  Starting file parsing...
+NOsh: Parsing READ section
+NOsh: Storing molecule 0 path mol0.pqr
+NOsh: Storing molecule 1 path mol1.pqr
+NOsh: Storing molecule 2 path complex-0_1.pqr
+NOsh: Done parsing READ section
+NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0)
+NOsh: Parsing ELEC section
+NOsh_parseMG: Parsing parameters for MG calculation
+NOsh_parseMG:  Parsing dime...
+PBEparm_parseToken:  trying dime...
+MGparm_parseToken:  trying dime...
+NOsh_parseMG:  Parsing grid...
+PBEparm_parseToken:  trying grid...
+MGparm_parseToken:  trying grid...
+NOsh_parseMG:  Parsing gcent...
+PBEparm_parseToken:  trying gcent...
+MGparm_parseToken:  trying gcent...
+NOsh_parseMG:  Parsing mol...
+PBEparm_parseToken:  trying mol...
+NOsh_parseMG:  Parsing lpbe...
+PBEparm_parseToken:  trying lpbe...
+NOsh: parsed lpbe
+NOsh_parseMG:  Parsing bcfl...
+PBEparm_parseToken:  trying bcfl...
+NOsh_parseMG:  Parsing pdie...
+PBEparm_parseToken:  trying pdie...
+NOsh_parseMG:  Parsing sdie...
+PBEparm_parseToken:  trying sdie...
+NOsh_parseMG:  Parsing chgm...
+PBEparm_parseToken:  trying chgm...
+MGparm_parseToken:  trying chgm...
+NOsh_parseMG:  Parsing srfm...
+PBEparm_parseToken:  trying srfm...
+NOsh_parseMG:  Parsing srad...
+PBEparm_parseToken:  trying srad...
+NOsh_parseMG:  Parsing swin...
+PBEparm_parseToken:  trying swin...
+NOsh_parseMG:  Parsing sdens...
+PBEparm_parseToken:  trying sdens...
+NOsh_parseMG:  Parsing temp...
+PBEparm_parseToken:  trying temp...
+NOsh_parseMG:  Parsing calcenergy...
+PBEparm_parseToken:  trying calcenergy...
+NOsh_parseMG:  Parsing calcforce...
+PBEparm_parseToken:  trying calcforce...
+NOsh_parseMG:  Parsing end...
+MGparm_check:  checking MGparm object of type 0.
+NOsh:  nlev = 5, dime = (65, 65, 65)
+NOsh: Done parsing ELEC section (nelec = 1)
+NOsh: Parsing ELEC section
+NOsh_parseMG: Parsing parameters for MG calculation
+NOsh_parseMG:  Parsing dime...
+PBEparm_parseToken:  trying dime...
+MGparm_parseToken:  trying dime...
+NOsh_parseMG:  Parsing grid...
+PBEparm_parseToken:  trying grid...
+MGparm_parseToken:  trying grid...
+NOsh_parseMG:  Parsing gcent...
+PBEparm_parseToken:  trying gcent...
+MGparm_parseToken:  trying gcent...
+NOsh_parseMG:  Parsing mol...
+PBEparm_parseToken:  trying mol...
+NOsh_parseMG:  Parsing lpbe...
+PBEparm_parseToken:  trying lpbe...
+NOsh: parsed lpbe
+NOsh_parseMG:  Parsing bcfl...
+PBEparm_parseToken:  trying bcfl...
+NOsh_parseMG:  Parsing pdie...
+PBEparm_parseToken:  trying pdie...
+NOsh_parseMG:  Parsing sdie...
+PBEparm_parseToken:  trying sdie...
+NOsh_parseMG:  Parsing chgm...
+PBEparm_parseToken:  trying chgm...
+MGparm_parseToken:  trying chgm...
+NOsh_parseMG:  Parsing srfm...
+PBEparm_parseToken:  trying srfm...
+NOsh_parseMG:  Parsing srad...
+PBEparm_parseToken:  trying srad...
+NOsh_parseMG:  Parsing swin...
+PBEparm_parseToken:  trying swin...
+NOsh_parseMG:  Parsing sdens...
+PBEparm_parseToken:  trying sdens...
+NOsh_parseMG:  Parsing temp...
+PBEparm_parseToken:  trying temp...
+NOsh_parseMG:  Parsing calcenergy...
+PBEparm_parseToken:  trying calcenergy...
+NOsh_parseMG:  Parsing calcforce...
+PBEparm_parseToken:  trying calcforce...
+NOsh_parseMG:  Parsing end...
+MGparm_check:  checking MGparm object of type 0.
+NOsh:  nlev = 5, dime = (65, 65, 65)
+NOsh: Done parsing ELEC section (nelec = 2)
+NOsh: Parsing ELEC section
+NOsh_parseMG: Parsing parameters for MG calculation
+NOsh_parseMG:  Parsing dime...
+PBEparm_parseToken:  trying dime...
+MGparm_parseToken:  trying dime...
+NOsh_parseMG:  Parsing grid...
+PBEparm_parseToken:  trying grid...
+MGparm_parseToken:  trying grid...
+NOsh_parseMG:  Parsing gcent...
+PBEparm_parseToken:  trying gcent...
+MGparm_parseToken:  trying gcent...
+NOsh_parseMG:  Parsing mol...
+PBEparm_parseToken:  trying mol...
+NOsh_parseMG:  Parsing lpbe...
+PBEparm_parseToken:  trying lpbe...
+NOsh: parsed lpbe
+NOsh_parseMG:  Parsing bcfl...
+PBEparm_parseToken:  trying bcfl...
+NOsh_parseMG:  Parsing pdie...
+PBEparm_parseToken:  trying pdie...
+NOsh_parseMG:  Parsing sdie...
+PBEparm_parseToken:  trying sdie...
+NOsh_parseMG:  Parsing chgm...
+PBEparm_parseToken:  trying chgm...
+MGparm_parseToken:  trying chgm...
+NOsh_parseMG:  Parsing srfm...
+PBEparm_parseToken:  trying srfm...
+NOsh_parseMG:  Parsing srad...
+PBEparm_parseToken:  trying srad...
+NOsh_parseMG:  Parsing swin...
+PBEparm_parseToken:  trying swin...
+NOsh_parseMG:  Parsing sdens...
+PBEparm_parseToken:  trying sdens...
+NOsh_parseMG:  Parsing temp...
+PBEparm_parseToken:  trying temp...
+NOsh_parseMG:  Parsing calcenergy...
+PBEparm_parseToken:  trying calcenergy...
+NOsh_parseMG:  Parsing calcforce...
+PBEparm_parseToken:  trying calcforce...
+NOsh_parseMG:  Parsing end...
+MGparm_check:  checking MGparm object of type 0.
+NOsh:  nlev = 5, dime = (65, 65, 65)
+NOsh: Done parsing ELEC section (nelec = 3)
+NOsh: Parsing PRINT section
+NOsh: Done parsing PRINT section
+NOsh: Done parsing PRINT section
+NOsh: Done parsing file (got QUIT)
+Valist_readPQR: Counted 1 atoms
+Valist_getStatistics:  Max atom coordinate:  (-3, 0, 0)
+Valist_getStatistics:  Min atom coordinate:  (-3, 0, 0)
+Valist_getStatistics:  Molecule center:  (-3, 0, 0)
+Valist_readPQR: Counted 1 atoms
+Valist_getStatistics:  Max atom coordinate:  (-2, 0, 0)
+Valist_getStatistics:  Min atom coordinate:  (-2, 0, 0)
+Valist_getStatistics:  Molecule center:  (-2, 0, 0)
+Valist_readPQR: Counted 2 atoms
+Valist_getStatistics:  Max atom coordinate:  (-2, 0, 0)
+Valist_getStatistics:  Min atom coordinate:  (-3, 0, 0)
+Valist_getStatistics:  Molecule center:  (-2.5, 0, 0)
+NOsh_setupCalc:  Mapping ELEC statement 0 (1) to calculation 0 (1)
+NOsh_setupCalc:  Mapping ELEC statement 1 (2) to calculation 1 (2)
+NOsh_setupCalc:  Mapping ELEC statement 2 (3) to calculation 2 (3)
+Vnm_tstart: starting timer 27 (Setup timer)..
+Setting up PBE object...
+Vpbe_ctor2:  solute radius = 0
+Vpbe_ctor2:  solute dimensions = 0 x 0 x 0
+Vpbe_ctor2:  solute charge = 1
+Vpbe_ctor2:  bulk ionic strength = 0
+Vpbe_ctor2:  xkappa = 0
+Vpbe_ctor2:  Debye length = 0
+Vpbe_ctor2:  zkappa2 = 0
+Vpbe_ctor2:  zmagic = 7042.98
+Vpbe_ctor2:  Constructing Vclist with 3 x 3 x 3 table
+Vclist_ctor2:  Using 3 x 3 x 3 hash table
+Vclist_ctor2:  automatic domain setup.
+Vclist_ctor2:  Using 0.8 max radius
+Vclist_setupGrid:  Grid lengths = (2.272, 2.272, 2.272)
+Vclist_setupGrid:  Grid lower corner = (-4.136, -1.136, -1.136)
+Vclist_assignAtoms:  Have 27 atom entries
+Vacc_storeParms:  Surf. density = 10
+Vacc_storeParms:  Max area = 8.04248
+Vacc_storeParms:  Using 80-point reference sphere
+Setting up PDE object...
+Vpmp_ctor2:  Using meth = 2, mgsolv = 1
+Setting PDE center to local center...
+Vpmg_fillco:  filling in source term.
+fillcoCharge:  Calling fillcoChargeSpline1...
+Vpmg_fillco:  filling in source term.
+Vpmg_fillco:  filling boundary arrays
+Vpmg_fillco:  done filling boundary arrays
+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.156400e-02
+Vnm_tstart: starting timer 28 (Solver timer)..
+Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
+Vbuildops: Fine: (065, 065, 065)
+Vbuildops: Operator stencil (lev, numdia) = (1, 4)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.248000e-03
+Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
+Vbuildops: Galer: (033, 033, 033)
+Vbuildops: Galer: (017, 017, 017)
+Vbuildops: Galer: (009, 009, 009)
+Vbuildops: Galer: (005, 005, 005)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.266000e-02
+Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.739200e-02
+Vprtstp: iteration = 0
+Vprtstp: relative residual = 1.000000e+00
+Vprtstp: contraction number = 1.000000e+00
+Vprtstp: iteration = 1
+Vprtstp: relative residual = 1.117158e-01
+Vprtstp: contraction number = 1.117158e-01
+Vprtstp: iteration = 2
+Vprtstp: relative residual = 1.151538e-02
+Vprtstp: contraction number = 1.030774e-01
+Vprtstp: iteration = 3
+Vprtstp: relative residual = 1.211573e-03
+Vprtstp: contraction number = 1.052135e-01
+Vprtstp: iteration = 4
+Vprtstp: relative residual = 1.284891e-04
+Vprtstp: contraction number = 1.060514e-01
+Vprtstp: iteration = 5
+Vprtstp: relative residual = 1.371257e-05
+Vprtstp: contraction number = 1.067217e-01
+Vprtstp: iteration = 6
+Vprtstp: relative residual = 1.472908e-06
+Vprtstp: contraction number = 1.074130e-01
+Vprtstp: iteration = 7
+Vprtstp: relative residual = 1.590269e-07
+Vprtstp: contraction number = 1.079680e-01
+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 9.875600e-02
+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.388240e-01
+Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)
+Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)
+Vpmg_setPart:  bflag[FRONT] = 0
+Vpmg_setPart:  bflag[BACK] = 0
+Vpmg_setPart:  bflag[LEFT] = 0
+Vpmg_setPart:  bflag[RIGHT] = 0
+Vpmg_setPart:  bflag[UP] = 0
+Vpmg_setPart:  bflag[DOWN] = 0
+Vnm_tstart: starting timer 29 (Energy timer)..
+Vpmg_energy:  calculating only q-phi energy
+Vpmg_energy:  qfEnergy = 7.887170085535E+01 kT
+Vpmg_qmEnergy:  Zero energy for zero ionic strength!
+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.248000e-03
+Vnm_tstart: starting timer 30 (Force timer)..
+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06
+Vnm_tstart: starting timer 27 (Setup timer)..
+Setting up PBE object...
+Vpbe_ctor2:  solute radius = 0
+Vpbe_ctor2:  solute dimensions = 0 x 0 x 0
+Vpbe_ctor2:  solute charge = 1
+Vpbe_ctor2:  bulk ionic strength = 0
+Vpbe_ctor2:  xkappa = 0
+Vpbe_ctor2:  Debye length = 0
+Vpbe_ctor2:  zkappa2 = 0
+Vpbe_ctor2:  zmagic = 7042.98
+Vpbe_ctor2:  Constructing Vclist with 3 x 3 x 3 table
+Vclist_ctor2:  Using 3 x 3 x 3 hash table
+Vclist_ctor2:  automatic domain setup.
+Vclist_ctor2:  Using 0.8 max radius
+Vclist_setupGrid:  Grid lengths = (2.272, 2.272, 2.272)
+Vclist_setupGrid:  Grid lower corner = (-3.136, -1.136, -1.136)
+Vclist_assignAtoms:  Have 27 atom entries
+Vacc_storeParms:  Surf. density = 10
+Vacc_storeParms:  Max area = 8.04248
+Vacc_storeParms:  Using 80-point reference sphere
+Setting up PDE object...
+Vpmp_ctor2:  Using meth = 2, mgsolv = 1
+Setting PDE center to local center...
+Vpmg_fillco:  filling in source term.
+fillcoCharge:  Calling fillcoChargeSpline1...
+Vpmg_fillco:  filling in source term.
+Vpmg_fillco:  filling boundary arrays
+Vpmg_fillco:  done filling boundary arrays
+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.262700e-02
+Vnm_tstart: starting timer 28 (Solver timer)..
+Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
+Vbuildops: Fine: (065, 065, 065)
+Vbuildops: Operator stencil (lev, numdia) = (1, 4)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.198000e-03
+Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
+Vbuildops: Galer: (033, 033, 033)
+Vbuildops: Galer: (017, 017, 017)
+Vbuildops: Galer: (009, 009, 009)
+Vbuildops: Galer: (005, 005, 005)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.132800e-02
+Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.083850e-01
+Vprtstp: iteration = 0
+Vprtstp: relative residual = 1.000000e+00
+Vprtstp: contraction number = 1.000000e+00
+Vprtstp: iteration = 1
+Vprtstp: relative residual = 1.116487e-01
+Vprtstp: contraction number = 1.116487e-01
+Vprtstp: iteration = 2
+Vprtstp: relative residual = 1.150253e-02
+Vprtstp: contraction number = 1.030244e-01
+Vprtstp: iteration = 3
+Vprtstp: relative residual = 1.210891e-03
+Vprtstp: contraction number = 1.052717e-01
+Vprtstp: iteration = 4
+Vprtstp: relative residual = 1.285247e-04
+Vprtstp: contraction number = 1.061405e-01
+Vprtstp: iteration = 5
+Vprtstp: relative residual = 1.373145e-05
+Vprtstp: contraction number = 1.068390e-01
+Vprtstp: iteration = 6
+Vprtstp: relative residual = 1.476968e-06
+Vprtstp: contraction number = 1.075610e-01
+Vprtstp: iteration = 7
+Vprtstp: relative residual = 1.596976e-07
+Vprtstp: contraction number = 1.081253e-01
+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 9.674900e-02
+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.335930e-01
+Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)
+Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)
+Vpmg_setPart:  bflag[FRONT] = 0
+Vpmg_setPart:  bflag[BACK] = 0
+Vpmg_setPart:  bflag[LEFT] = 0
+Vpmg_setPart:  bflag[RIGHT] = 0
+Vpmg_setPart:  bflag[UP] = 0
+Vpmg_setPart:  bflag[DOWN] = 0
+Vnm_tstart: starting timer 29 (Energy timer)..
+Vpmg_energy:  calculating only q-phi energy
+Vpmg_energy:  qfEnergy = 7.241648379021E+01 kT
+Vpmg_qmEnergy:  Zero energy for zero ionic strength!
+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.470000e-03
+Vnm_tstart: starting timer 30 (Force timer)..
+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06
+Vnm_tstart: starting timer 27 (Setup timer)..
+Setting up PBE object...
+Vpbe_ctor2:  solute radius = 0.5
+Vpbe_ctor2:  solute dimensions = 1 x 0 x 0
+Vpbe_ctor2:  solute charge = 2
+Vpbe_ctor2:  bulk ionic strength = 0
+Vpbe_ctor2:  xkappa = 0
+Vpbe_ctor2:  Debye length = 0
+Vpbe_ctor2:  zkappa2 = 0
+Vpbe_ctor2:  zmagic = 7042.98
+Vpbe_ctor2:  Constructing Vclist with 3 x 3 x 3 table
+Vclist_ctor2:  Using 3 x 3 x 3 hash table
+Vclist_ctor2:  automatic domain setup.
+Vclist_ctor2:  Using 0.8 max radius
+Vclist_setupGrid:  Grid lengths = (3.272, 2.272, 2.272)
+Vclist_setupGrid:  Grid lower corner = (-4.136, -1.136, -1.136)
+Vclist_assignAtoms:  Have 54 atom entries
+Vacc_storeParms:  Surf. density = 10
+Vacc_storeParms:  Max area = 8.04248
+Vacc_storeParms:  Using 80-point reference sphere
+Setting up PDE object...
+Vpmp_ctor2:  Using meth = 2, mgsolv = 1
+Setting PDE center to local center...
+Vpmg_fillco:  filling in source term.
+fillcoCharge:  Calling fillcoChargeSpline1...
+Vpmg_fillco:  filling in source term.
+Vpmg_fillco:  filling boundary arrays
+Vpmg_fillco:  done filling boundary arrays
+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.257700e-02
+Vnm_tstart: starting timer 28 (Solver timer)..
+Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
+Vbuildops: Fine: (065, 065, 065)
+Vbuildops: Operator stencil (lev, numdia) = (1, 4)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.264000e-03
+Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
+Vbuildops: Galer: (033, 033, 033)
+Vbuildops: Galer: (017, 017, 017)
+Vbuildops: Galer: (009, 009, 009)
+Vbuildops: Galer: (005, 005, 005)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.730600e-02
+Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.544460e-01
+Vprtstp: iteration = 0
+Vprtstp: relative residual = 1.000000e+00
+Vprtstp: contraction number = 1.000000e+00
+Vprtstp: iteration = 1
+Vprtstp: relative residual = 1.110273e-01
+Vprtstp: contraction number = 1.110273e-01
+Vprtstp: iteration = 2
+Vprtstp: relative residual = 1.143155e-02
+Vprtstp: contraction number = 1.029617e-01
+Vprtstp: iteration = 3
+Vprtstp: relative residual = 1.203363e-03
+Vprtstp: contraction number = 1.052668e-01
+Vprtstp: iteration = 4
+Vprtstp: relative residual = 1.276645e-04
+Vprtstp: contraction number = 1.060898e-01
+Vprtstp: iteration = 5
+Vprtstp: relative residual = 1.362985e-05
+Vprtstp: contraction number = 1.067630e-01
+Vprtstp: iteration = 6
+Vprtstp: relative residual = 1.464818e-06
+Vprtstp: contraction number = 1.074713e-01
+Vprtstp: iteration = 7
+Vprtstp: relative residual = 1.582462e-07
+Vprtstp: contraction number = 1.080314e-01
+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 9.976500e-02
+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.333000e-01
+Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)
+Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)
+Vpmg_setPart:  bflag[FRONT] = 0
+Vpmg_setPart:  bflag[BACK] = 0
+Vpmg_setPart:  bflag[LEFT] = 0
+Vpmg_setPart:  bflag[RIGHT] = 0
+Vpmg_setPart:  bflag[UP] = 0
+Vpmg_setPart:  bflag[DOWN] = 0
+Vnm_tstart: starting timer 29 (Energy timer)..
+Vpmg_energy:  calculating only q-phi energy
+Vpmg_energy:  qfEnergy = 1.660589930493E+02 kT
+Vpmg_qmEnergy:  Zero energy for zero ionic strength!
+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.049000e-03
+Vnm_tstart: starting timer 30 (Force timer)..
+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06
+printEnergy:  Performing global reduction (sum)
+Vcom_reduce:  Not compiled with MPI, doing simple copy.
+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.546300e-01
+##############################################################################
+# MC-shell I/O capture file.
+# Creation Date and Time:  Fri Apr 29 19:48:48 2022
+
+##############################################################################
+Hello world from PE 0
+Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..
+NOsh_parseInput:  Starting file parsing...
+NOsh: Parsing READ section
+NOsh: Storing molecule 0 path mol0.pqr
+NOsh: Storing molecule 1 path mol2.pqr
+NOsh: Storing molecule 2 path complex-0_2.pqr
+NOsh: Done parsing READ section
+NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0)
+NOsh: Parsing ELEC section
+NOsh_parseMG: Parsing parameters for MG calculation
+NOsh_parseMG:  Parsing dime...
+PBEparm_parseToken:  trying dime...
+MGparm_parseToken:  trying dime...
+NOsh_parseMG:  Parsing grid...
+PBEparm_parseToken:  trying grid...
+MGparm_parseToken:  trying grid...
+NOsh_parseMG:  Parsing gcent...
+PBEparm_parseToken:  trying gcent...
+MGparm_parseToken:  trying gcent...
+NOsh_parseMG:  Parsing mol...
+PBEparm_parseToken:  trying mol...
+NOsh_parseMG:  Parsing lpbe...
+PBEparm_parseToken:  trying lpbe...
+NOsh: parsed lpbe
+NOsh_parseMG:  Parsing bcfl...
+PBEparm_parseToken:  trying bcfl...
+NOsh_parseMG:  Parsing pdie...
+PBEparm_parseToken:  trying pdie...
+NOsh_parseMG:  Parsing sdie...
+PBEparm_parseToken:  trying sdie...
+NOsh_parseMG:  Parsing chgm...
+PBEparm_parseToken:  trying chgm...
+MGparm_parseToken:  trying chgm...
+NOsh_parseMG:  Parsing srfm...
+PBEparm_parseToken:  trying srfm...
+NOsh_parseMG:  Parsing srad...
+PBEparm_parseToken:  trying srad...
+NOsh_parseMG:  Parsing swin...
+PBEparm_parseToken:  trying swin...
+NOsh_parseMG:  Parsing sdens...
+PBEparm_parseToken:  trying sdens...
+NOsh_parseMG:  Parsing temp...
+PBEparm_parseToken:  trying temp...
+NOsh_parseMG:  Parsing calcenergy...
+PBEparm_parseToken:  trying calcenergy...
+NOsh_parseMG:  Parsing calcforce...
+PBEparm_parseToken:  trying calcforce...
+NOsh_parseMG:  Parsing end...
+MGparm_check:  checking MGparm object of type 0.
+NOsh:  nlev = 5, dime = (65, 65, 65)
+NOsh: Done parsing ELEC section (nelec = 1)
+NOsh: Parsing ELEC section
+NOsh_parseMG: Parsing parameters for MG calculation
+NOsh_parseMG:  Parsing dime...
+PBEparm_parseToken:  trying dime...
+MGparm_parseToken:  trying dime...
+NOsh_parseMG:  Parsing grid...
+PBEparm_parseToken:  trying grid...
+MGparm_parseToken:  trying grid...
+NOsh_parseMG:  Parsing gcent...
+PBEparm_parseToken:  trying gcent...
+MGparm_parseToken:  trying gcent...
+NOsh_parseMG:  Parsing mol...
+PBEparm_parseToken:  trying mol...
+NOsh_parseMG:  Parsing lpbe...
+PBEparm_parseToken:  trying lpbe...
+NOsh: parsed lpbe
+NOsh_parseMG:  Parsing bcfl...
+PBEparm_parseToken:  trying bcfl...
+NOsh_parseMG:  Parsing pdie...
+PBEparm_parseToken:  trying pdie...
+NOsh_parseMG:  Parsing sdie...
+PBEparm_parseToken:  trying sdie...
+NOsh_parseMG:  Parsing chgm...
+PBEparm_parseToken:  trying chgm...
+MGparm_parseToken:  trying chgm...
+NOsh_parseMG:  Parsing srfm...
+PBEparm_parseToken:  trying srfm...
+NOsh_parseMG:  Parsing srad...
+PBEparm_parseToken:  trying srad...
+NOsh_parseMG:  Parsing swin...
+PBEparm_parseToken:  trying swin...
+NOsh_parseMG:  Parsing sdens...
+PBEparm_parseToken:  trying sdens...
+NOsh_parseMG:  Parsing temp...
+PBEparm_parseToken:  trying temp...
+NOsh_parseMG:  Parsing calcenergy...
+PBEparm_parseToken:  trying calcenergy...
+NOsh_parseMG:  Parsing calcforce...
+PBEparm_parseToken:  trying calcforce...
+NOsh_parseMG:  Parsing end...
+MGparm_check:  checking MGparm object of type 0.
+NOsh:  nlev = 5, dime = (65, 65, 65)
+NOsh: Done parsing ELEC section (nelec = 2)
+NOsh: Parsing ELEC section
+NOsh_parseMG: Parsing parameters for MG calculation
+NOsh_parseMG:  Parsing dime...
+PBEparm_parseToken:  trying dime...
+MGparm_parseToken:  trying dime...
+NOsh_parseMG:  Parsing grid...
+PBEparm_parseToken:  trying grid...
+MGparm_parseToken:  trying grid...
+NOsh_parseMG:  Parsing gcent...
+PBEparm_parseToken:  trying gcent...
+MGparm_parseToken:  trying gcent...
+NOsh_parseMG:  Parsing mol...
+PBEparm_parseToken:  trying mol...
+NOsh_parseMG:  Parsing lpbe...
+PBEparm_parseToken:  trying lpbe...
+NOsh: parsed lpbe
+NOsh_parseMG:  Parsing bcfl...
+PBEparm_parseToken:  trying bcfl...
+NOsh_parseMG:  Parsing pdie...
+PBEparm_parseToken:  trying pdie...
+NOsh_parseMG:  Parsing sdie...
+PBEparm_parseToken:  trying sdie...
+NOsh_parseMG:  Parsing chgm...
+PBEparm_parseToken:  trying chgm...
+MGparm_parseToken:  trying chgm...
+NOsh_parseMG:  Parsing srfm...
+PBEparm_parseToken:  trying srfm...
+NOsh_parseMG:  Parsing srad...
+PBEparm_parseToken:  trying srad...
+NOsh_parseMG:  Parsing swin...
+PBEparm_parseToken:  trying swin...
+NOsh_parseMG:  Parsing sdens...
+PBEparm_parseToken:  trying sdens...
+NOsh_parseMG:  Parsing temp...
+PBEparm_parseToken:  trying temp...
+NOsh_parseMG:  Parsing calcenergy...
+PBEparm_parseToken:  trying calcenergy...
+NOsh_parseMG:  Parsing calcforce...
+PBEparm_parseToken:  trying calcforce...
+NOsh_parseMG:  Parsing end...
+MGparm_check:  checking MGparm object of type 0.
+NOsh:  nlev = 5, dime = (65, 65, 65)
+NOsh: Done parsing ELEC section (nelec = 3)
+NOsh: Parsing PRINT section
+NOsh: Done parsing PRINT section
+NOsh: Done parsing PRINT section
+NOsh: Done parsing file (got QUIT)
+Valist_readPQR: Counted 1 atoms
+Valist_getStatistics:  Max atom coordinate:  (-3, 0, 0)
+Valist_getStatistics:  Min atom coordinate:  (-3, 0, 0)
+Valist_getStatistics:  Molecule center:  (-3, 0, 0)
+Valist_readPQR: Counted 1 atoms
+Valist_getStatistics:  Max atom coordinate:  (-1, 0, 0)
+Valist_getStatistics:  Min atom coordinate:  (-1, 0, 0)
+Valist_getStatistics:  Molecule center:  (-1, 0, 0)
+Valist_readPQR: Counted 2 atoms
+Valist_getStatistics:  Max atom coordinate:  (-1, 0, 0)
+Valist_getStatistics:  Min atom coordinate:  (-3, 0, 0)
+Valist_getStatistics:  Molecule center:  (-2, 0, 0)
+NOsh_setupCalc:  Mapping ELEC statement 0 (1) to calculation 0 (1)
+NOsh_setupCalc:  Mapping ELEC statement 1 (2) to calculation 1 (2)
+NOsh_setupCalc:  Mapping ELEC statement 2 (3) to calculation 2 (3)
+Vnm_tstart: starting timer 27 (Setup timer)..
+Setting up PBE object...
+Vpbe_ctor2:  solute radius = 0
+Vpbe_ctor2:  solute dimensions = 0 x 0 x 0
+Vpbe_ctor2:  solute charge = 1
+Vpbe_ctor2:  bulk ionic strength = 0
+Vpbe_ctor2:  xkappa = 0
+Vpbe_ctor2:  Debye length = 0
+Vpbe_ctor2:  zkappa2 = 0
+Vpbe_ctor2:  zmagic = 7042.98
+Vpbe_ctor2:  Constructing Vclist with 3 x 3 x 3 table
+Vclist_ctor2:  Using 3 x 3 x 3 hash table
+Vclist_ctor2:  automatic domain setup.
+Vclist_ctor2:  Using 0.8 max radius
+Vclist_setupGrid:  Grid lengths = (2.272, 2.272, 2.272)
+Vclist_setupGrid:  Grid lower corner = (-4.136, -1.136, -1.136)
+Vclist_assignAtoms:  Have 27 atom entries
+Vacc_storeParms:  Surf. density = 10
+Vacc_storeParms:  Max area = 8.04248
+Vacc_storeParms:  Using 80-point reference sphere
+Setting up PDE object...
+Vpmp_ctor2:  Using meth = 2, mgsolv = 1
+Setting PDE center to local center...
+Vpmg_fillco:  filling in source term.
+fillcoCharge:  Calling fillcoChargeSpline1...
+Vpmg_fillco:  filling in source term.
+Vpmg_fillco:  filling boundary arrays
+Vpmg_fillco:  done filling boundary arrays
+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.106800e-02
+Vnm_tstart: starting timer 28 (Solver timer)..
+Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
+Vbuildops: Fine: (065, 065, 065)
+Vbuildops: Operator stencil (lev, numdia) = (1, 4)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.850000e-03
+Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
+Vbuildops: Galer: (033, 033, 033)
+Vbuildops: Galer: (017, 017, 017)
+Vbuildops: Galer: (009, 009, 009)
+Vbuildops: Galer: (005, 005, 005)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.636300e-02
+Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.979400e-02
+Vprtstp: iteration = 0
+Vprtstp: relative residual = 1.000000e+00
+Vprtstp: contraction number = 1.000000e+00
+Vprtstp: iteration = 1
+Vprtstp: relative residual = 1.117158e-01
+Vprtstp: contraction number = 1.117158e-01
+Vprtstp: iteration = 2
+Vprtstp: relative residual = 1.151538e-02
+Vprtstp: contraction number = 1.030774e-01
+Vprtstp: iteration = 3
+Vprtstp: relative residual = 1.211573e-03
+Vprtstp: contraction number = 1.052135e-01
+Vprtstp: iteration = 4
+Vprtstp: relative residual = 1.284891e-04
+Vprtstp: contraction number = 1.060514e-01
+Vprtstp: iteration = 5
+Vprtstp: relative residual = 1.371257e-05
+Vprtstp: contraction number = 1.067217e-01
+Vprtstp: iteration = 6
+Vprtstp: relative residual = 1.472908e-06
+Vprtstp: contraction number = 1.074130e-01
+Vprtstp: iteration = 7
+Vprtstp: relative residual = 1.590269e-07
+Vprtstp: contraction number = 1.079680e-01
+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 9.960800e-02
+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.425720e-01
+Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)
+Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)
+Vpmg_setPart:  bflag[FRONT] = 0
+Vpmg_setPart:  bflag[BACK] = 0
+Vpmg_setPart:  bflag[LEFT] = 0
+Vpmg_setPart:  bflag[RIGHT] = 0
+Vpmg_setPart:  bflag[UP] = 0
+Vpmg_setPart:  bflag[DOWN] = 0
+Vnm_tstart: starting timer 29 (Energy timer)..
+Vpmg_energy:  calculating only q-phi energy
+Vpmg_energy:  qfEnergy = 7.887170085535E+01 kT
+Vpmg_qmEnergy:  Zero energy for zero ionic strength!
+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.473000e-03
+Vnm_tstart: starting timer 30 (Force timer)..
+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06
+Vnm_tstart: starting timer 27 (Setup timer)..
+Setting up PBE object...
+Vpbe_ctor2:  solute radius = 0
+Vpbe_ctor2:  solute dimensions = 0 x 0 x 0
+Vpbe_ctor2:  solute charge = 1
+Vpbe_ctor2:  bulk ionic strength = 0
+Vpbe_ctor2:  xkappa = 0
+Vpbe_ctor2:  Debye length = 0
+Vpbe_ctor2:  zkappa2 = 0
+Vpbe_ctor2:  zmagic = 7042.98
+Vpbe_ctor2:  Constructing Vclist with 3 x 3 x 3 table
+Vclist_ctor2:  Using 3 x 3 x 3 hash table
+Vclist_ctor2:  automatic domain setup.
+Vclist_ctor2:  Using 0.8 max radius
+Vclist_setupGrid:  Grid lengths = (2.272, 2.272, 2.272)
+Vclist_setupGrid:  Grid lower corner = (-2.136, -1.136, -1.136)
+Vclist_assignAtoms:  Have 27 atom entries
+Vacc_storeParms:  Surf. density = 10
+Vacc_storeParms:  Max area = 8.04248
+Vacc_storeParms:  Using 80-point reference sphere
+Setting up PDE object...
+Vpmp_ctor2:  Using meth = 2, mgsolv = 1
+Setting PDE center to local center...
+Vpmg_fillco:  filling in source term.
+fillcoCharge:  Calling fillcoChargeSpline1...
+Vpmg_fillco:  filling in source term.
+Vpmg_fillco:  filling boundary arrays
+Vpmg_fillco:  done filling boundary arrays
+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.250100e-02
+Vnm_tstart: starting timer 28 (Solver timer)..
+Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
+Vbuildops: Fine: (065, 065, 065)
+Vbuildops: Operator stencil (lev, numdia) = (1, 4)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.291000e-03
+Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
+Vbuildops: Galer: (033, 033, 033)
+Vbuildops: Galer: (017, 017, 017)
+Vbuildops: Galer: (009, 009, 009)
+Vbuildops: Galer: (005, 005, 005)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.401400e-02
+Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.146360e-01
+Vprtstp: iteration = 0
+Vprtstp: relative residual = 1.000000e+00
+Vprtstp: contraction number = 1.000000e+00
+Vprtstp: iteration = 1
+Vprtstp: relative residual = 1.115116e-01
+Vprtstp: contraction number = 1.115116e-01
+Vprtstp: iteration = 2
+Vprtstp: relative residual = 1.148798e-02
+Vprtstp: contraction number = 1.030205e-01
+Vprtstp: iteration = 3
+Vprtstp: relative residual = 1.210191e-03
+Vprtstp: contraction number = 1.053440e-01
+Vprtstp: iteration = 4
+Vprtstp: relative residual = 1.284884e-04
+Vprtstp: contraction number = 1.061720e-01
+Vprtstp: iteration = 5
+Vprtstp: relative residual = 1.372980e-05
+Vprtstp: contraction number = 1.068563e-01
+Vprtstp: iteration = 6
+Vprtstp: relative residual = 1.477070e-06
+Vprtstp: contraction number = 1.075813e-01
+Vprtstp: iteration = 7
+Vprtstp: relative residual = 1.597562e-07
+Vprtstp: contraction number = 1.081575e-01
+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 9.812900e-02
+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.376920e-01
+Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)
+Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)
+Vpmg_setPart:  bflag[FRONT] = 0
+Vpmg_setPart:  bflag[BACK] = 0
+Vpmg_setPart:  bflag[LEFT] = 0
+Vpmg_setPart:  bflag[RIGHT] = 0
+Vpmg_setPart:  bflag[UP] = 0
+Vpmg_setPart:  bflag[DOWN] = 0
+Vnm_tstart: starting timer 29 (Energy timer)..
+Vpmg_energy:  calculating only q-phi energy
+Vpmg_energy:  qfEnergy = 8.209948502984E+01 kT
+Vpmg_qmEnergy:  Zero energy for zero ionic strength!
+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.118000e-03
+Vnm_tstart: starting timer 30 (Force timer)..
+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06
+Vnm_tstart: starting timer 27 (Setup timer)..
+Setting up PBE object...
+Vpbe_ctor2:  solute radius = 1
+Vpbe_ctor2:  solute dimensions = 2 x 0 x 0
+Vpbe_ctor2:  solute charge = 2
+Vpbe_ctor2:  bulk ionic strength = 0
+Vpbe_ctor2:  xkappa = 0
+Vpbe_ctor2:  Debye length = 0
+Vpbe_ctor2:  zkappa2 = 0
+Vpbe_ctor2:  zmagic = 7042.98
+Vpbe_ctor2:  Constructing Vclist with 4 x 3 x 3 table
+Vclist_ctor2:  Using 4 x 3 x 3 hash table
+Vclist_ctor2:  automatic domain setup.
+Vclist_ctor2:  Using 0.8 max radius
+Vclist_setupGrid:  Grid lengths = (4.272, 2.272, 2.272)
+Vclist_setupGrid:  Grid lower corner = (-4.136, -1.136, -1.136)
+Vclist_assignAtoms:  Have 54 atom entries
+Vacc_storeParms:  Surf. density = 10
+Vacc_storeParms:  Max area = 8.04248
+Vacc_storeParms:  Using 80-point reference sphere
+Setting up PDE object...
+Vpmp_ctor2:  Using meth = 2, mgsolv = 1
+Setting PDE center to local center...
+Vpmg_fillco:  filling in source term.
+fillcoCharge:  Calling fillcoChargeSpline1...
+Vpmg_fillco:  filling in source term.
+Vpmg_fillco:  filling boundary arrays
+Vpmg_fillco:  done filling boundary arrays
+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.254900e-02
+Vnm_tstart: starting timer 28 (Solver timer)..
+Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
+Vbuildops: Fine: (065, 065, 065)
+Vbuildops: Operator stencil (lev, numdia) = (1, 4)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.363000e-03
+Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
+Vbuildops: Galer: (033, 033, 033)
+Vbuildops: Galer: (017, 017, 017)
+Vbuildops: Galer: (009, 009, 009)
+Vbuildops: Galer: (005, 005, 005)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.912600e-02
+Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.637570e-01
+Vprtstp: iteration = 0
+Vprtstp: relative residual = 1.000000e+00
+Vprtstp: contraction number = 1.000000e+00
+Vprtstp: iteration = 1
+Vprtstp: relative residual = 1.112280e-01
+Vprtstp: contraction number = 1.112280e-01
+Vprtstp: iteration = 2
+Vprtstp: relative residual = 1.145843e-02
+Vprtstp: contraction number = 1.030175e-01
+Vprtstp: iteration = 3
+Vprtstp: relative residual = 1.206047e-03
+Vprtstp: contraction number = 1.052541e-01
+Vprtstp: iteration = 4
+Vprtstp: relative residual = 1.279108e-04
+Vprtstp: contraction number = 1.060578e-01
+Vprtstp: iteration = 5
+Vprtstp: relative residual = 1.365147e-05
+Vprtstp: contraction number = 1.067265e-01
+Vprtstp: iteration = 6
+Vprtstp: relative residual = 1.466596e-06
+Vprtstp: contraction number = 1.074314e-01
+Vprtstp: iteration = 7
+Vprtstp: relative residual = 1.583845e-07
+Vprtstp: contraction number = 1.079946e-01
+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.001780e-01
+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.358670e-01
+Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)
+Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)
+Vpmg_setPart:  bflag[FRONT] = 0
+Vpmg_setPart:  bflag[BACK] = 0
+Vpmg_setPart:  bflag[LEFT] = 0
+Vpmg_setPart:  bflag[RIGHT] = 0
+Vpmg_setPart:  bflag[UP] = 0
+Vpmg_setPart:  bflag[DOWN] = 0
+Vnm_tstart: starting timer 29 (Energy timer)..
+Vpmg_energy:  calculating only q-phi energy
+Vpmg_energy:  qfEnergy = 1.681569832028E+02 kT
+Vpmg_qmEnergy:  Zero energy for zero ionic strength!
+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.268000e-03
+Vnm_tstart: starting timer 30 (Force timer)..
+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06
+printEnergy:  Performing global reduction (sum)
+Vcom_reduce:  Not compiled with MPI, doing simple copy.
+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.642680e-01
+##############################################################################
+# MC-shell I/O capture file.
+# Creation Date and Time:  Fri Apr 29 19:48:49 2022
+
+##############################################################################
+Hello world from PE 0
+Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..
+NOsh_parseInput:  Starting file parsing...
+NOsh: Parsing READ section
+NOsh: Storing molecule 0 path mol0.pqr
+NOsh: Storing molecule 1 path mol3.pqr
+NOsh: Storing molecule 2 path complex-0_3.pqr
+NOsh: Done parsing READ section
+NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0)
+NOsh: Parsing ELEC section
+NOsh_parseMG: Parsing parameters for MG calculation
+NOsh_parseMG:  Parsing dime...
+PBEparm_parseToken:  trying dime...
+MGparm_parseToken:  trying dime...
+NOsh_parseMG:  Parsing grid...
+PBEparm_parseToken:  trying grid...
+MGparm_parseToken:  trying grid...
+NOsh_parseMG:  Parsing gcent...
+PBEparm_parseToken:  trying gcent...
+MGparm_parseToken:  trying gcent...
+NOsh_parseMG:  Parsing mol...
+PBEparm_parseToken:  trying mol...
+NOsh_parseMG:  Parsing lpbe...
+PBEparm_parseToken:  trying lpbe...
+NOsh: parsed lpbe
+NOsh_parseMG:  Parsing bcfl...
+PBEparm_parseToken:  trying bcfl...
+NOsh_parseMG:  Parsing pdie...
+PBEparm_parseToken:  trying pdie...
+NOsh_parseMG:  Parsing sdie...
+PBEparm_parseToken:  trying sdie...
+NOsh_parseMG:  Parsing chgm...
+PBEparm_parseToken:  trying chgm...
+MGparm_parseToken:  trying chgm...
+NOsh_parseMG:  Parsing srfm...
+PBEparm_parseToken:  trying srfm...
+NOsh_parseMG:  Parsing srad...
+PBEparm_parseToken:  trying srad...
+NOsh_parseMG:  Parsing swin...
+PBEparm_parseToken:  trying swin...
+NOsh_parseMG:  Parsing sdens...
+PBEparm_parseToken:  trying sdens...
+NOsh_parseMG:  Parsing temp...
+PBEparm_parseToken:  trying temp...
+NOsh_parseMG:  Parsing calcenergy...
+PBEparm_parseToken:  trying calcenergy...
+NOsh_parseMG:  Parsing calcforce...
+PBEparm_parseToken:  trying calcforce...
+NOsh_parseMG:  Parsing end...
+MGparm_check:  checking MGparm object of type 0.
+NOsh:  nlev = 5, dime = (65, 65, 65)
+NOsh: Done parsing ELEC section (nelec = 1)
+NOsh: Parsing ELEC section
+NOsh_parseMG: Parsing parameters for MG calculation
+NOsh_parseMG:  Parsing dime...
+PBEparm_parseToken:  trying dime...
+MGparm_parseToken:  trying dime...
+NOsh_parseMG:  Parsing grid...
+PBEparm_parseToken:  trying grid...
+MGparm_parseToken:  trying grid...
+NOsh_parseMG:  Parsing gcent...
+PBEparm_parseToken:  trying gcent...
+MGparm_parseToken:  trying gcent...
+NOsh_parseMG:  Parsing mol...
+PBEparm_parseToken:  trying mol...
+NOsh_parseMG:  Parsing lpbe...
+PBEparm_parseToken:  trying lpbe...
+NOsh: parsed lpbe
+NOsh_parseMG:  Parsing bcfl...
+PBEparm_parseToken:  trying bcfl...
+NOsh_parseMG:  Parsing pdie...
+PBEparm_parseToken:  trying pdie...
+NOsh_parseMG:  Parsing sdie...
+PBEparm_parseToken:  trying sdie...
+NOsh_parseMG:  Parsing chgm...
+PBEparm_parseToken:  trying chgm...
+MGparm_parseToken:  trying chgm...
+NOsh_parseMG:  Parsing srfm...
+PBEparm_parseToken:  trying srfm...
+NOsh_parseMG:  Parsing srad...
+PBEparm_parseToken:  trying srad...
+NOsh_parseMG:  Parsing swin...
+PBEparm_parseToken:  trying swin...
+NOsh_parseMG:  Parsing sdens...
+PBEparm_parseToken:  trying sdens...
+NOsh_parseMG:  Parsing temp...
+PBEparm_parseToken:  trying temp...
+NOsh_parseMG:  Parsing calcenergy...
+PBEparm_parseToken:  trying calcenergy...
+NOsh_parseMG:  Parsing calcforce...
+PBEparm_parseToken:  trying calcforce...
+NOsh_parseMG:  Parsing end...
+MGparm_check:  checking MGparm object of type 0.
+NOsh:  nlev = 5, dime = (65, 65, 65)
+NOsh: Done parsing ELEC section (nelec = 2)
+NOsh: Parsing ELEC section
+NOsh_parseMG: Parsing parameters for MG calculation
+NOsh_parseMG:  Parsing dime...
+PBEparm_parseToken:  trying dime...
+MGparm_parseToken:  trying dime...
+NOsh_parseMG:  Parsing grid...
+PBEparm_parseToken:  trying grid...
+MGparm_parseToken:  trying grid...
+NOsh_parseMG:  Parsing gcent...
+PBEparm_parseToken:  trying gcent...
+MGparm_parseToken:  trying gcent...
+NOsh_parseMG:  Parsing mol...
+PBEparm_parseToken:  trying mol...
+NOsh_parseMG:  Parsing lpbe...
+PBEparm_parseToken:  trying lpbe...
+NOsh: parsed lpbe
+NOsh_parseMG:  Parsing bcfl...
+PBEparm_parseToken:  trying bcfl...
+NOsh_parseMG:  Parsing pdie...
+PBEparm_parseToken:  trying pdie...
+NOsh_parseMG:  Parsing sdie...
+PBEparm_parseToken:  trying sdie...
+NOsh_parseMG:  Parsing chgm...
+PBEparm_parseToken:  trying chgm...
+MGparm_parseToken:  trying chgm...
+NOsh_parseMG:  Parsing srfm...
+PBEparm_parseToken:  trying srfm...
+NOsh_parseMG:  Parsing srad...
+PBEparm_parseToken:  trying srad...
+NOsh_parseMG:  Parsing swin...
+PBEparm_parseToken:  trying swin...
+NOsh_parseMG:  Parsing sdens...
+PBEparm_parseToken:  trying sdens...
+NOsh_parseMG:  Parsing temp...
+PBEparm_parseToken:  trying temp...
+NOsh_parseMG:  Parsing calcenergy...
+PBEparm_parseToken:  trying calcenergy...
+NOsh_parseMG:  Parsing calcforce...
+PBEparm_parseToken:  trying calcforce...
+NOsh_parseMG:  Parsing end...
+MGparm_check:  checking MGparm object of type 0.
+NOsh:  nlev = 5, dime = (65, 65, 65)
+NOsh: Done parsing ELEC section (nelec = 3)
+NOsh: Parsing PRINT section
+NOsh: Done parsing PRINT section
+NOsh: Done parsing PRINT section
+NOsh: Done parsing file (got QUIT)
+Valist_readPQR: Counted 1 atoms
+Valist_getStatistics:  Max atom coordinate:  (-3, 0, 0)
+Valist_getStatistics:  Min atom coordinate:  (-3, 0, 0)
+Valist_getStatistics:  Molecule center:  (-3, 0, 0)
+Valist_readPQR: Counted 1 atoms
+Valist_getStatistics:  Max atom coordinate:  (0, 0, 0)
+Valist_getStatistics:  Min atom coordinate:  (0, 0, 0)
+Valist_getStatistics:  Molecule center:  (0, 0, 0)
+Valist_readPQR: Counted 2 atoms
+Valist_getStatistics:  Max atom coordinate:  (0, 0, 0)
+Valist_getStatistics:  Min atom coordinate:  (-3, 0, 0)
+Valist_getStatistics:  Molecule center:  (-1.5, 0, 0)
+NOsh_setupCalc:  Mapping ELEC statement 0 (1) to calculation 0 (1)
+NOsh_setupCalc:  Mapping ELEC statement 1 (2) to calculation 1 (2)
+NOsh_setupCalc:  Mapping ELEC statement 2 (3) to calculation 2 (3)
+Vnm_tstart: starting timer 27 (Setup timer)..
+Setting up PBE object...
+Vpbe_ctor2:  solute radius = 0
+Vpbe_ctor2:  solute dimensions = 0 x 0 x 0
+Vpbe_ctor2:  solute charge = 1
+Vpbe_ctor2:  bulk ionic strength = 0
+Vpbe_ctor2:  xkappa = 0
+Vpbe_ctor2:  Debye length = 0
+Vpbe_ctor2:  zkappa2 = 0
+Vpbe_ctor2:  zmagic = 7042.98
+Vpbe_ctor2:  Constructing Vclist with 3 x 3 x 3 table
+Vclist_ctor2:  Using 3 x 3 x 3 hash table
+Vclist_ctor2:  automatic domain setup.
+Vclist_ctor2:  Using 0.8 max radius
+Vclist_setupGrid:  Grid lengths = (2.272, 2.272, 2.272)
+Vclist_setupGrid:  Grid lower corner = (-4.136, -1.136, -1.136)
+Vclist_assignAtoms:  Have 27 atom entries
+Vacc_storeParms:  Surf. density = 10
+Vacc_storeParms:  Max area = 8.04248
+Vacc_storeParms:  Using 80-point reference sphere
+Setting up PDE object...
+Vpmp_ctor2:  Using meth = 2, mgsolv = 1
+Setting PDE center to local center...
+Vpmg_fillco:  filling in source term.
+fillcoCharge:  Calling fillcoChargeSpline1...
+Vpmg_fillco:  filling in source term.
+Vpmg_fillco:  filling boundary arrays
+Vpmg_fillco:  done filling boundary arrays
+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.088300e-02
+Vnm_tstart: starting timer 28 (Solver timer)..
+Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
+Vbuildops: Fine: (065, 065, 065)
+Vbuildops: Operator stencil (lev, numdia) = (1, 4)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.068000e-03
+Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
+Vbuildops: Galer: (033, 033, 033)
+Vbuildops: Galer: (017, 017, 017)
+Vbuildops: Galer: (009, 009, 009)
+Vbuildops: Galer: (005, 005, 005)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.270000e-02
+Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.608500e-02
+Vprtstp: iteration = 0
+Vprtstp: relative residual = 1.000000e+00
+Vprtstp: contraction number = 1.000000e+00
+Vprtstp: iteration = 1
+Vprtstp: relative residual = 1.117158e-01
+Vprtstp: contraction number = 1.117158e-01
+Vprtstp: iteration = 2
+Vprtstp: relative residual = 1.151538e-02
+Vprtstp: contraction number = 1.030774e-01
+Vprtstp: iteration = 3
+Vprtstp: relative residual = 1.211573e-03
+Vprtstp: contraction number = 1.052135e-01
+Vprtstp: iteration = 4
+Vprtstp: relative residual = 1.284891e-04
+Vprtstp: contraction number = 1.060514e-01
+Vprtstp: iteration = 5
+Vprtstp: relative residual = 1.371257e-05
+Vprtstp: contraction number = 1.067217e-01
+Vprtstp: iteration = 6
+Vprtstp: relative residual = 1.472908e-06
+Vprtstp: contraction number = 1.074130e-01
+Vprtstp: iteration = 7
+Vprtstp: relative residual = 1.590269e-07
+Vprtstp: contraction number = 1.079680e-01
+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.044240e-01
+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.445430e-01
+Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)
+Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)
+Vpmg_setPart:  bflag[FRONT] = 0
+Vpmg_setPart:  bflag[BACK] = 0
+Vpmg_setPart:  bflag[LEFT] = 0
+Vpmg_setPart:  bflag[RIGHT] = 0
+Vpmg_setPart:  bflag[UP] = 0
+Vpmg_setPart:  bflag[DOWN] = 0
+Vnm_tstart: starting timer 29 (Energy timer)..
+Vpmg_energy:  calculating only q-phi energy
+Vpmg_energy:  qfEnergy = 7.887170085535E+01 kT
+Vpmg_qmEnergy:  Zero energy for zero ionic strength!
+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.454000e-03
+Vnm_tstart: starting timer 30 (Force timer)..
+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06
+Vnm_tstart: starting timer 27 (Setup timer)..
+Setting up PBE object...
+Vpbe_ctor2:  solute radius = 0
+Vpbe_ctor2:  solute dimensions = 0 x 0 x 0
+Vpbe_ctor2:  solute charge = 1
+Vpbe_ctor2:  bulk ionic strength = 0
+Vpbe_ctor2:  xkappa = 0
+Vpbe_ctor2:  Debye length = 0
+Vpbe_ctor2:  zkappa2 = 0
+Vpbe_ctor2:  zmagic = 7042.98
+Vpbe_ctor2:  Constructing Vclist with 3 x 3 x 3 table
+Vclist_ctor2:  Using 3 x 3 x 3 hash table
+Vclist_ctor2:  automatic domain setup.
+Vclist_ctor2:  Using 0.8 max radius
+Vclist_setupGrid:  Grid lengths = (2.272, 2.272, 2.272)
+Vclist_setupGrid:  Grid lower corner = (-1.136, -1.136, -1.136)
+Vclist_assignAtoms:  Have 27 atom entries
+Vacc_storeParms:  Surf. density = 10
+Vacc_storeParms:  Max area = 8.04248
+Vacc_storeParms:  Using 80-point reference sphere
+Setting up PDE object...
+Vpmp_ctor2:  Using meth = 2, mgsolv = 1
+Setting PDE center to local center...
+Vpmg_fillco:  filling in source term.
+fillcoCharge:  Calling fillcoChargeSpline1...
+Vpmg_fillco:  filling in source term.
+Vpmg_fillco:  filling boundary arrays
+Vpmg_fillco:  done filling boundary arrays
+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.281400e-02
+Vnm_tstart: starting timer 28 (Solver timer)..
+Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
+Vbuildops: Fine: (065, 065, 065)
+Vbuildops: Operator stencil (lev, numdia) = (1, 4)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.646000e-03
+Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
+Vbuildops: Galer: (033, 033, 033)
+Vbuildops: Galer: (017, 017, 017)
+Vbuildops: Galer: (009, 009, 009)
+Vbuildops: Galer: (005, 005, 005)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.482000e-02
+Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.179090e-01
+Vprtstp: iteration = 0
+Vprtstp: relative residual = 1.000000e+00
+Vprtstp: contraction number = 1.000000e+00
+Vprtstp: iteration = 1
+Vprtstp: relative residual = 1.122494e-01
+Vprtstp: contraction number = 1.122494e-01
+Vprtstp: iteration = 2
+Vprtstp: relative residual = 1.156196e-02
+Vprtstp: contraction number = 1.030024e-01
+Vprtstp: iteration = 3
+Vprtstp: relative residual = 1.217663e-03
+Vprtstp: contraction number = 1.053163e-01
+Vprtstp: iteration = 4
+Vprtstp: relative residual = 1.292438e-04
+Vprtstp: contraction number = 1.061408e-01
+Vprtstp: iteration = 5
+Vprtstp: relative residual = 1.380655e-05
+Vprtstp: contraction number = 1.068256e-01
+Vprtstp: iteration = 6
+Vprtstp: relative residual = 1.484900e-06
+Vprtstp: contraction number = 1.075504e-01
+Vprtstp: iteration = 7
+Vprtstp: relative residual = 1.605755e-07
+Vprtstp: contraction number = 1.081389e-01
+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.016960e-01
+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.431790e-01
+Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)
+Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)
+Vpmg_setPart:  bflag[FRONT] = 0
+Vpmg_setPart:  bflag[BACK] = 0
+Vpmg_setPart:  bflag[LEFT] = 0
+Vpmg_setPart:  bflag[RIGHT] = 0
+Vpmg_setPart:  bflag[UP] = 0
+Vpmg_setPart:  bflag[DOWN] = 0
+Vnm_tstart: starting timer 29 (Energy timer)..
+Vpmg_energy:  calculating only q-phi energy
+Vpmg_energy:  qfEnergy = 1.079207063662E+02 kT
+Vpmg_qmEnergy:  Zero energy for zero ionic strength!
+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.383000e-03
+Vnm_tstart: starting timer 30 (Force timer)..
+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06
+Vnm_tstart: starting timer 27 (Setup timer)..
+Setting up PBE object...
+Vpbe_ctor2:  solute radius = 1.5
+Vpbe_ctor2:  solute dimensions = 3 x 0 x 0
+Vpbe_ctor2:  solute charge = 2
+Vpbe_ctor2:  bulk ionic strength = 0
+Vpbe_ctor2:  xkappa = 0
+Vpbe_ctor2:  Debye length = 0
+Vpbe_ctor2:  zkappa2 = 0
+Vpbe_ctor2:  zmagic = 7042.98
+Vpbe_ctor2:  Constructing Vclist with 6 x 3 x 3 table
+Vclist_ctor2:  Using 6 x 3 x 3 hash table
+Vclist_ctor2:  automatic domain setup.
+Vclist_ctor2:  Using 0.8 max radius
+Vclist_setupGrid:  Grid lengths = (5.272, 2.272, 2.272)
+Vclist_setupGrid:  Grid lower corner = (-4.136, -1.136, -1.136)
+Vclist_assignAtoms:  Have 54 atom entries
+Vacc_storeParms:  Surf. density = 10
+Vacc_storeParms:  Max area = 8.04248
+Vacc_storeParms:  Using 80-point reference sphere
+Setting up PDE object...
+Vpmp_ctor2:  Using meth = 2, mgsolv = 1
+Setting PDE center to local center...
+Vpmg_fillco:  filling in source term.
+fillcoCharge:  Calling fillcoChargeSpline1...
+Vpmg_fillco:  filling in source term.
+Vpmg_fillco:  filling boundary arrays
+Vpmg_fillco:  done filling boundary arrays
+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.326500e-02
+Vnm_tstart: starting timer 28 (Solver timer)..
+Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
+Vbuildops: Fine: (065, 065, 065)
+Vbuildops: Operator stencil (lev, numdia) = (1, 4)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.926000e-03
+Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
+Vbuildops: Galer: (033, 033, 033)
+Vbuildops: Galer: (017, 017, 017)
+Vbuildops: Galer: (009, 009, 009)
+Vbuildops: Galer: (005, 005, 005)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.984800e-02
+Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.717770e-01
+Vprtstp: iteration = 0
+Vprtstp: relative residual = 1.000000e+00
+Vprtstp: contraction number = 1.000000e+00
+Vprtstp: iteration = 1
+Vprtstp: relative residual = 1.117126e-01
+Vprtstp: contraction number = 1.117126e-01
+Vprtstp: iteration = 2
+Vprtstp: relative residual = 1.151034e-02
+Vprtstp: contraction number = 1.030352e-01
+Vprtstp: iteration = 3
+Vprtstp: relative residual = 1.211194e-03
+Vprtstp: contraction number = 1.052267e-01
+Vprtstp: iteration = 4
+Vprtstp: relative residual = 1.284280e-04
+Vprtstp: contraction number = 1.060342e-01
+Vprtstp: iteration = 5
+Vprtstp: relative residual = 1.370613e-05
+Vprtstp: contraction number = 1.067223e-01
+Vprtstp: iteration = 6
+Vprtstp: relative residual = 1.472511e-06
+Vprtstp: contraction number = 1.074345e-01
+Vprtstp: iteration = 7
+Vprtstp: relative residual = 1.590395e-07
+Vprtstp: contraction number = 1.080057e-01
+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 9.847200e-02
+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.343690e-01
+Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)
+Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)
+Vpmg_setPart:  bflag[FRONT] = 0
+Vpmg_setPart:  bflag[BACK] = 0
+Vpmg_setPart:  bflag[LEFT] = 0
+Vpmg_setPart:  bflag[RIGHT] = 0
+Vpmg_setPart:  bflag[UP] = 0
+Vpmg_setPart:  bflag[DOWN] = 0
+Vnm_tstart: starting timer 29 (Energy timer)..
+Vpmg_energy:  calculating only q-phi energy
+Vpmg_energy:  qfEnergy = 1.915601904303E+02 kT
+Vpmg_qmEnergy:  Zero energy for zero ionic strength!
+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.211000e-03
+Vnm_tstart: starting timer 30 (Force timer)..
+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06
+printEnergy:  Performing global reduction (sum)
+Vcom_reduce:  Not compiled with MPI, doing simple copy.
+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.718600e-01
+##############################################################################
+# MC-shell I/O capture file.
+# Creation Date and Time:  Fri Apr 29 19:48:49 2022
+
+##############################################################################
+Hello world from PE 0
+Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..
+NOsh_parseInput:  Starting file parsing...
+NOsh: Parsing READ section
+NOsh: Storing molecule 0 path mol0.pqr
+NOsh: Storing molecule 1 path mol4.pqr
+NOsh: Storing molecule 2 path complex-0_4.pqr
+NOsh: Done parsing READ section
+NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0)
+NOsh: Parsing ELEC section
+NOsh_parseMG: Parsing parameters for MG calculation
+NOsh_parseMG:  Parsing dime...
+PBEparm_parseToken:  trying dime...
+MGparm_parseToken:  trying dime...
+NOsh_parseMG:  Parsing grid...
+PBEparm_parseToken:  trying grid...
+MGparm_parseToken:  trying grid...
+NOsh_parseMG:  Parsing gcent...
+PBEparm_parseToken:  trying gcent...
+MGparm_parseToken:  trying gcent...
+NOsh_parseMG:  Parsing mol...
+PBEparm_parseToken:  trying mol...
+NOsh_parseMG:  Parsing lpbe...
+PBEparm_parseToken:  trying lpbe...
+NOsh: parsed lpbe
+NOsh_parseMG:  Parsing bcfl...
+PBEparm_parseToken:  trying bcfl...
+NOsh_parseMG:  Parsing pdie...
+PBEparm_parseToken:  trying pdie...
+NOsh_parseMG:  Parsing sdie...
+PBEparm_parseToken:  trying sdie...
+NOsh_parseMG:  Parsing chgm...
+PBEparm_parseToken:  trying chgm...
+MGparm_parseToken:  trying chgm...
+NOsh_parseMG:  Parsing srfm...
+PBEparm_parseToken:  trying srfm...
+NOsh_parseMG:  Parsing srad...
+PBEparm_parseToken:  trying srad...
+NOsh_parseMG:  Parsing swin...
+PBEparm_parseToken:  trying swin...
+NOsh_parseMG:  Parsing sdens...
+PBEparm_parseToken:  trying sdens...
+NOsh_parseMG:  Parsing temp...
+PBEparm_parseToken:  trying temp...
+NOsh_parseMG:  Parsing calcenergy...
+PBEparm_parseToken:  trying calcenergy...
+NOsh_parseMG:  Parsing calcforce...
+PBEparm_parseToken:  trying calcforce...
+NOsh_parseMG:  Parsing end...
+MGparm_check:  checking MGparm object of type 0.
+NOsh:  nlev = 5, dime = (65, 65, 65)
+NOsh: Done parsing ELEC section (nelec = 1)
+NOsh: Parsing ELEC section
+NOsh_parseMG: Parsing parameters for MG calculation
+NOsh_parseMG:  Parsing dime...
+PBEparm_parseToken:  trying dime...
+MGparm_parseToken:  trying dime...
+NOsh_parseMG:  Parsing grid...
+PBEparm_parseToken:  trying grid...
+MGparm_parseToken:  trying grid...
+NOsh_parseMG:  Parsing gcent...
+PBEparm_parseToken:  trying gcent...
+MGparm_parseToken:  trying gcent...
+NOsh_parseMG:  Parsing mol...
+PBEparm_parseToken:  trying mol...
+NOsh_parseMG:  Parsing lpbe...
+PBEparm_parseToken:  trying lpbe...
+NOsh: parsed lpbe
+NOsh_parseMG:  Parsing bcfl...
+PBEparm_parseToken:  trying bcfl...
+NOsh_parseMG:  Parsing pdie...
+PBEparm_parseToken:  trying pdie...
+NOsh_parseMG:  Parsing sdie...
+PBEparm_parseToken:  trying sdie...
+NOsh_parseMG:  Parsing chgm...
+PBEparm_parseToken:  trying chgm...
+MGparm_parseToken:  trying chgm...
+NOsh_parseMG:  Parsing srfm...
+PBEparm_parseToken:  trying srfm...
+NOsh_parseMG:  Parsing srad...
+PBEparm_parseToken:  trying srad...
+NOsh_parseMG:  Parsing swin...
+PBEparm_parseToken:  trying swin...
+NOsh_parseMG:  Parsing sdens...
+PBEparm_parseToken:  trying sdens...
+NOsh_parseMG:  Parsing temp...
+PBEparm_parseToken:  trying temp...
+NOsh_parseMG:  Parsing calcenergy...
+PBEparm_parseToken:  trying calcenergy...
+NOsh_parseMG:  Parsing calcforce...
+PBEparm_parseToken:  trying calcforce...
+NOsh_parseMG:  Parsing end...
+MGparm_check:  checking MGparm object of type 0.
+NOsh:  nlev = 5, dime = (65, 65, 65)
+NOsh: Done parsing ELEC section (nelec = 2)
+NOsh: Parsing ELEC section
+NOsh_parseMG: Parsing parameters for MG calculation
+NOsh_parseMG:  Parsing dime...
+PBEparm_parseToken:  trying dime...
+MGparm_parseToken:  trying dime...
+NOsh_parseMG:  Parsing grid...
+PBEparm_parseToken:  trying grid...
+MGparm_parseToken:  trying grid...
+NOsh_parseMG:  Parsing gcent...
+PBEparm_parseToken:  trying gcent...
+MGparm_parseToken:  trying gcent...
+NOsh_parseMG:  Parsing mol...
+PBEparm_parseToken:  trying mol...
+NOsh_parseMG:  Parsing lpbe...
+PBEparm_parseToken:  trying lpbe...
+NOsh: parsed lpbe
+NOsh_parseMG:  Parsing bcfl...
+PBEparm_parseToken:  trying bcfl...
+NOsh_parseMG:  Parsing pdie...
+PBEparm_parseToken:  trying pdie...
+NOsh_parseMG:  Parsing sdie...
+PBEparm_parseToken:  trying sdie...
+NOsh_parseMG:  Parsing chgm...
+PBEparm_parseToken:  trying chgm...
+MGparm_parseToken:  trying chgm...
+NOsh_parseMG:  Parsing srfm...
+PBEparm_parseToken:  trying srfm...
+NOsh_parseMG:  Parsing srad...
+PBEparm_parseToken:  trying srad...
+NOsh_parseMG:  Parsing swin...
+PBEparm_parseToken:  trying swin...
+NOsh_parseMG:  Parsing sdens...
+PBEparm_parseToken:  trying sdens...
+NOsh_parseMG:  Parsing temp...
+PBEparm_parseToken:  trying temp...
+NOsh_parseMG:  Parsing calcenergy...
+PBEparm_parseToken:  trying calcenergy...
+NOsh_parseMG:  Parsing calcforce...
+PBEparm_parseToken:  trying calcforce...
+NOsh_parseMG:  Parsing end...
+MGparm_check:  checking MGparm object of type 0.
+NOsh:  nlev = 5, dime = (65, 65, 65)
+NOsh: Done parsing ELEC section (nelec = 3)
+NOsh: Parsing PRINT section
+NOsh: Done parsing PRINT section
+NOsh: Done parsing PRINT section
+NOsh: Done parsing file (got QUIT)
+Valist_readPQR: Counted 1 atoms
+Valist_getStatistics:  Max atom coordinate:  (-3, 0, 0)
+Valist_getStatistics:  Min atom coordinate:  (-3, 0, 0)
+Valist_getStatistics:  Molecule center:  (-3, 0, 0)
+Valist_readPQR: Counted 1 atoms
+Valist_getStatistics:  Max atom coordinate:  (1, 0, 0)
+Valist_getStatistics:  Min atom coordinate:  (1, 0, 0)
+Valist_getStatistics:  Molecule center:  (1, 0, 0)
+Valist_readPQR: Counted 2 atoms
+Valist_getStatistics:  Max atom coordinate:  (1, 0, 0)
+Valist_getStatistics:  Min atom coordinate:  (-3, 0, 0)
+Valist_getStatistics:  Molecule center:  (-1, 0, 0)
+NOsh_setupCalc:  Mapping ELEC statement 0 (1) to calculation 0 (1)
+NOsh_setupCalc:  Mapping ELEC statement 1 (2) to calculation 1 (2)
+NOsh_setupCalc:  Mapping ELEC statement 2 (3) to calculation 2 (3)
+Vnm_tstart: starting timer 27 (Setup timer)..
+Setting up PBE object...
+Vpbe_ctor2:  solute radius = 0
+Vpbe_ctor2:  solute dimensions = 0 x 0 x 0
+Vpbe_ctor2:  solute charge = 1
+Vpbe_ctor2:  bulk ionic strength = 0
+Vpbe_ctor2:  xkappa = 0
+Vpbe_ctor2:  Debye length = 0
+Vpbe_ctor2:  zkappa2 = 0
+Vpbe_ctor2:  zmagic = 7042.98
+Vpbe_ctor2:  Constructing Vclist with 3 x 3 x 3 table
+Vclist_ctor2:  Using 3 x 3 x 3 hash table
+Vclist_ctor2:  automatic domain setup.
+Vclist_ctor2:  Using 0.8 max radius
+Vclist_setupGrid:  Grid lengths = (2.272, 2.272, 2.272)
+Vclist_setupGrid:  Grid lower corner = (-4.136, -1.136, -1.136)
+Vclist_assignAtoms:  Have 27 atom entries
+Vacc_storeParms:  Surf. density = 10
+Vacc_storeParms:  Max area = 8.04248
+Vacc_storeParms:  Using 80-point reference sphere
+Setting up PDE object...
+Vpmp_ctor2:  Using meth = 2, mgsolv = 1
+Setting PDE center to local center...
+Vpmg_fillco:  filling in source term.
+fillcoCharge:  Calling fillcoChargeSpline1...
+Vpmg_fillco:  filling in source term.
+Vpmg_fillco:  filling boundary arrays
+Vpmg_fillco:  done filling boundary arrays
+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.057100e-02
+Vnm_tstart: starting timer 28 (Solver timer)..
+Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
+Vbuildops: Fine: (065, 065, 065)
+Vbuildops: Operator stencil (lev, numdia) = (1, 4)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.012800e-02
+Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
+Vbuildops: Galer: (033, 033, 033)
+Vbuildops: Galer: (017, 017, 017)
+Vbuildops: Galer: (009, 009, 009)
+Vbuildops: Galer: (005, 005, 005)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.386400e-02
+Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.629800e-02
+Vprtstp: iteration = 0
+Vprtstp: relative residual = 1.000000e+00
+Vprtstp: contraction number = 1.000000e+00
+Vprtstp: iteration = 1
+Vprtstp: relative residual = 1.117158e-01
+Vprtstp: contraction number = 1.117158e-01
+Vprtstp: iteration = 2
+Vprtstp: relative residual = 1.151538e-02
+Vprtstp: contraction number = 1.030774e-01
+Vprtstp: iteration = 3
+Vprtstp: relative residual = 1.211573e-03
+Vprtstp: contraction number = 1.052135e-01
+Vprtstp: iteration = 4
+Vprtstp: relative residual = 1.284891e-04
+Vprtstp: contraction number = 1.060514e-01
+Vprtstp: iteration = 5
+Vprtstp: relative residual = 1.371257e-05
+Vprtstp: contraction number = 1.067217e-01
+Vprtstp: iteration = 6
+Vprtstp: relative residual = 1.472908e-06
+Vprtstp: contraction number = 1.074130e-01
+Vprtstp: iteration = 7
+Vprtstp: relative residual = 1.590269e-07
+Vprtstp: contraction number = 1.079680e-01
+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.029860e-01
+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.446970e-01
+Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)
+Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)
+Vpmg_setPart:  bflag[FRONT] = 0
+Vpmg_setPart:  bflag[BACK] = 0
+Vpmg_setPart:  bflag[LEFT] = 0
+Vpmg_setPart:  bflag[RIGHT] = 0
+Vpmg_setPart:  bflag[UP] = 0
+Vpmg_setPart:  bflag[DOWN] = 0
+Vnm_tstart: starting timer 29 (Energy timer)..
+Vpmg_energy:  calculating only q-phi energy
+Vpmg_energy:  qfEnergy = 7.887170085535E+01 kT
+Vpmg_qmEnergy:  Zero energy for zero ionic strength!
+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.110000e-03
+Vnm_tstart: starting timer 30 (Force timer)..
+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06
+Vnm_tstart: starting timer 27 (Setup timer)..
+Setting up PBE object...
+Vpbe_ctor2:  solute radius = 0
+Vpbe_ctor2:  solute dimensions = 0 x 0 x 0
+Vpbe_ctor2:  solute charge = 1
+Vpbe_ctor2:  bulk ionic strength = 0
+Vpbe_ctor2:  xkappa = 0
+Vpbe_ctor2:  Debye length = 0
+Vpbe_ctor2:  zkappa2 = 0
+Vpbe_ctor2:  zmagic = 7042.98
+Vpbe_ctor2:  Constructing Vclist with 3 x 3 x 3 table
+Vclist_ctor2:  Using 3 x 3 x 3 hash table
+Vclist_ctor2:  automatic domain setup.
+Vclist_ctor2:  Using 0.8 max radius
+Vclist_setupGrid:  Grid lengths = (2.272, 2.272, 2.272)
+Vclist_setupGrid:  Grid lower corner = (-0.136, -1.136, -1.136)
+Vclist_assignAtoms:  Have 27 atom entries
+Vacc_storeParms:  Surf. density = 10
+Vacc_storeParms:  Max area = 8.04248
+Vacc_storeParms:  Using 80-point reference sphere
+Setting up PDE object...
+Vpmp_ctor2:  Using meth = 2, mgsolv = 1
+Setting PDE center to local center...
+Vpmg_fillco:  filling in source term.
+fillcoCharge:  Calling fillcoChargeSpline1...
+Vpmg_fillco:  filling in source term.
+Vpmg_fillco:  filling boundary arrays
+Vpmg_fillco:  done filling boundary arrays
+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.241600e-02
+Vnm_tstart: starting timer 28 (Solver timer)..
+Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
+Vbuildops: Fine: (065, 065, 065)
+Vbuildops: Operator stencil (lev, numdia) = (1, 4)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.511000e-03
+Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
+Vbuildops: Galer: (033, 033, 033)
+Vbuildops: Galer: (017, 017, 017)
+Vbuildops: Galer: (009, 009, 009)
+Vbuildops: Galer: (005, 005, 005)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.679700e-02
+Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.150390e-01
+Vprtstp: iteration = 0
+Vprtstp: relative residual = 1.000000e+00
+Vprtstp: contraction number = 1.000000e+00
+Vprtstp: iteration = 1
+Vprtstp: relative residual = 1.115116e-01
+Vprtstp: contraction number = 1.115116e-01
+Vprtstp: iteration = 2
+Vprtstp: relative residual = 1.148798e-02
+Vprtstp: contraction number = 1.030205e-01
+Vprtstp: iteration = 3
+Vprtstp: relative residual = 1.210191e-03
+Vprtstp: contraction number = 1.053440e-01
+Vprtstp: iteration = 4
+Vprtstp: relative residual = 1.284884e-04
+Vprtstp: contraction number = 1.061720e-01
+Vprtstp: iteration = 5
+Vprtstp: relative residual = 1.372980e-05
+Vprtstp: contraction number = 1.068563e-01
+Vprtstp: iteration = 6
+Vprtstp: relative residual = 1.477070e-06
+Vprtstp: contraction number = 1.075813e-01
+Vprtstp: iteration = 7
+Vprtstp: relative residual = 1.597562e-07
+Vprtstp: contraction number = 1.081575e-01
+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.101640e-01
+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.509890e-01
+Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)
+Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)
+Vpmg_setPart:  bflag[FRONT] = 0
+Vpmg_setPart:  bflag[BACK] = 0
+Vpmg_setPart:  bflag[LEFT] = 0
+Vpmg_setPart:  bflag[RIGHT] = 0
+Vpmg_setPart:  bflag[UP] = 0
+Vpmg_setPart:  bflag[DOWN] = 0
+Vnm_tstart: starting timer 29 (Energy timer)..
+Vpmg_energy:  calculating only q-phi energy
+Vpmg_energy:  qfEnergy = 8.209948502984E+01 kT
+Vpmg_qmEnergy:  Zero energy for zero ionic strength!
+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.375000e-03
+Vnm_tstart: starting timer 30 (Force timer)..
+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06
+Vnm_tstart: starting timer 27 (Setup timer)..
+Setting up PBE object...
+Vpbe_ctor2:  solute radius = 2
+Vpbe_ctor2:  solute dimensions = 4 x 0 x 0
+Vpbe_ctor2:  solute charge = 2
+Vpbe_ctor2:  bulk ionic strength = 0
+Vpbe_ctor2:  xkappa = 0
+Vpbe_ctor2:  Debye length = 0
+Vpbe_ctor2:  zkappa2 = 0
+Vpbe_ctor2:  zmagic = 7042.98
+Vpbe_ctor2:  Constructing Vclist with 8 x 3 x 3 table
+Vclist_ctor2:  Using 8 x 3 x 3 hash table
+Vclist_ctor2:  automatic domain setup.
+Vclist_ctor2:  Using 0.8 max radius
+Vclist_setupGrid:  Grid lengths = (6.272, 2.272, 2.272)
+Vclist_setupGrid:  Grid lower corner = (-4.136, -1.136, -1.136)
+Vclist_assignAtoms:  Have 72 atom entries
+Vacc_storeParms:  Surf. density = 10
+Vacc_storeParms:  Max area = 8.04248
+Vacc_storeParms:  Using 80-point reference sphere
+Setting up PDE object...
+Vpmp_ctor2:  Using meth = 2, mgsolv = 1
+Setting PDE center to local center...
+Vpmg_fillco:  filling in source term.
+fillcoCharge:  Calling fillcoChargeSpline1...
+Vpmg_fillco:  filling in source term.
+Vpmg_fillco:  filling boundary arrays
+Vpmg_fillco:  done filling boundary arrays
+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.403500e-02
+Vnm_tstart: starting timer 28 (Solver timer)..
+Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..
+Vbuildops: Fine: (065, 065, 065)
+Vbuildops: Operator stencil (lev, numdia) = (1, 4)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.655000e-03
+Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..
+Vbuildops: Galer: (033, 033, 033)
+Vbuildops: Galer: (017, 017, 017)
+Vbuildops: Galer: (009, 009, 009)
+Vbuildops: Galer: (005, 005, 005)
+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 3.087300e-02
+Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..
+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.801800e-01
+Vprtstp: iteration = 0
+Vprtstp: relative residual = 1.000000e+00
+Vprtstp: contraction number = 1.000000e+00
+Vprtstp: iteration = 1
+Vprtstp: relative residual = 1.113661e-01
+Vprtstp: contraction number = 1.113661e-01
+Vprtstp: iteration = 2
+Vprtstp: relative residual = 1.147756e-02
+Vprtstp: contraction number = 1.030616e-01
+Vprtstp: iteration = 3
+Vprtstp: relative residual = 1.208293e-03
+Vprtstp: contraction number = 1.052743e-01
+Vprtstp: iteration = 4
+Vprtstp: relative residual = 1.281804e-04
+Vprtstp: contraction number = 1.060839e-01
+Vprtstp: iteration = 5
+Vprtstp: relative residual = 1.368393e-05
+Vprtstp: contraction number = 1.067553e-01
+Vprtstp: iteration = 6
+Vprtstp: relative residual = 1.470482e-06
+Vprtstp: contraction number = 1.074604e-01
+Vprtstp: iteration = 7
+Vprtstp: relative residual = 1.588507e-07
+Vprtstp: contraction number = 1.080263e-01
+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.084300e-01
+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.462190e-01
+Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)
+Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)
+Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)
+Vpmg_setPart:  bflag[FRONT] = 0
+Vpmg_setPart:  bflag[BACK] = 0
+Vpmg_setPart:  bflag[LEFT] = 0
+Vpmg_setPart:  bflag[RIGHT] = 0
+Vpmg_setPart:  bflag[UP] = 0
+Vpmg_setPart:  bflag[DOWN] = 0
+Vnm_tstart: starting timer 29 (Energy timer)..
+Vpmg_energy:  calculating only q-phi energy
+Vpmg_energy:  qfEnergy = 1.645453654146E+02 kT
+Vpmg_qmEnergy:  Zero energy for zero ionic strength!
+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.406000e-03
+Vnm_tstart: starting timer 30 (Force timer)..
+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06
+printEnergy:  Performing global reduction (sum)
+Vcom_reduce:  Not compiled with MPI, doing simple copy.
+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.908930e-01

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/mol0.pqr

@@ -0,0 +1 @@
+ATOM      1  I   ION     1      -3.000    0.000   0.000  1.00 0.00

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/mol1.pqr

@@ -0,0 +1 @@
+ATOM      1  I   ION     1      -2.000    0.000   0.000  1.00 0.00

model/comp_surface/tools/transfer/APBS-3.4.1.Linux/share/apbs/examples/point-pmf/mol2.pqr

@@ -0,0 +1 @@
+ATOM      1  I   ION     1      -1.000    0.000   0.000  1.00 0.00