diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000000000000000000000000000000000000..22f16e533e467292b131d74b4fe634decc1f889b
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,3 @@
+*.pdb filter=lfs diff=lfs merge=lfs -text
+*.sdf filter=lfs diff=lfs merge=lfs -text
+*.csv filter=lfs diff=lfs merge=lfs -text
diff --git a/fep_benchmark_inputs/README.md b/fep_benchmark_inputs/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..f1d756a22d012a8e7020d47bd055b725e3a75e3a
--- /dev/null
+++ b/fep_benchmark_inputs/README.md
@@ -0,0 +1,23 @@
+# Inputs for running the binding free energy benchmark
+The inputs for the free energy benchmark are divided into two sections:
+* `fep_plus_inputs/` which contains the inputs for the FEP+ software (e.g. `fmp` files) and the scripts required to
+run the benchmark.
+* `structure_inputs/` which contain structural inputs in a format can be read by many computational chemistry platforms
+(i.e. `PDB` and `sdf` files).
+
+This benchmark data set was constructed and validated using FEP+ and the data in the `structure_inputs` was derived from
+the FEP+ `fmp` graph files..
+
+## Arrangment of the input files
+The benchmark data set consists of a number of congeneric series that have been grouped based on the publication where 
+the inputs were based on. As documented in the supporting information of the [accompanying manuscript](https://doi.org/10.26434/chemrxiv-2022-p2vpg),
+many systems were modified from their original source. 
+
+## Metadata
+Details on the congeneric series subset, file naming scheme, protein name, original PDB reference, experimental binding
+affinity dynamic range, number of input structures, and the DOI of the source on the source where the structures were 
+taken from, can be found in the file below:
+* `benchmark_metadata.csv`
+
+The `Number of nodes` column in `benchmark_metadata.csv` refers to the number of ligand structural inputs. Some ligands 
+had multiple structural inputs as they were represented by multiple rotamers or protomer/tautomers.
\ No newline at end of file
diff --git a/fep_benchmark_inputs/benchmark_metadata.csv b/fep_benchmark_inputs/benchmark_metadata.csv
new file mode 100644
index 0000000000000000000000000000000000000000..1310bf8a1635951e1cd275a1aa7d5a3cdd59c919
--- /dev/null
+++ b/fep_benchmark_inputs/benchmark_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:cdad4307424417583e8f1e27e195d56e8e5c88cae7354e52f713b16a1f07c07d
+size 8065
diff --git a/fep_benchmark_inputs/fep_plus_inputs/README.md b/fep_benchmark_inputs/fep_plus_inputs/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..9b12ff93391f8390e41529d7ce79beac846aca60
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/README.md
@@ -0,0 +1,42 @@
+# Benchmark inputs for FEP+
+
+This directory contains the FEP+ input files (`.fmp`s) and submission scripts for running the extended benchmark data
+set. There are 103 `fmp` files for a wide range of targets and congeneric series. The input 
+files are separated into 14 separate directories that reflect the origin of the data sets. Every `fmp` file in this 
+directory forms is part of the benchmark. 
+
+## Contents
+* `apply_all_corrections.sh` Apply post simulation corrections to all output fmp files that require them. This 
+script also collects the names and locations of the output fmp files into text files which facilitate analysis.
+* `post_simulation_corrections.md` A description of the post simulation corrections. These corrections are 
+applied with `apply_all_corrections.sh`.
+* `binding_mode_correction.py` The script to automatically apply binding mode corrections. This is needed for some
+systems.
+* `README.md`. This file. 
+
+## Subset directories
+The names of each directory and the corresponding subset title in the [accompanying manuscript](https://doi.org/10.26434/chemrxiv-2022-p2vpg).
+* `bayer_macrocycles/`: Bayer Macrocycles
+* `charge_annhil/`: FEP+ charge change set
+* `fragments/`: FEP+ fragment data set
+* `gpcrs/`: GPCRs
+* `jacs_set/`: FEP+ R-group set
+* `janssen_bace/`: Janssen BACE1 data sets
+* `macrocycles/`: FEP+ macrocycles
+* `mcs_docking/`: MCS docking sets
+* `merck/`: The public Merck data set
+* `misc/`: Miscellaneous data sets
+* `opls_stress/`: OPLS stress set
+* `opls_ddag`: OPLS private drug discovery data sets
+* `scaffold_hoping/`: FEP+ scaffold hopping
+* `waterset/`: FEP+ buried water set
+
+### Subset directory contents
+Each directory has the following files
+* `subset_metadata.csv`. Metadata on each subsystem, the naming scheme and the PDB each model was based on.  
+* `*.fmp` files. These are FEP+ format maps/perturbation graphs
+* `setup_and_run.sh`. A submission script for all FEP+ maps in the that uses the settings described in the accompanying paper. 
+* ` run_all_corrections.sh`. A script to run all corrections on the fmp files in that directory.
+* Additional files related to post-processing corrections to the results.
+
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/apply_all_corrections.sh b/fep_benchmark_inputs/fep_plus_inputs/apply_all_corrections.sh
new file mode 100755
index 0000000000000000000000000000000000000000..16e878b3a1eb6c95d17d719b7718e39b20f2f012
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/apply_all_corrections.sh
@@ -0,0 +1,192 @@
+###################
+# Bayer macrocycles
+###################
+echo 'Collecting Bayer macrocycle data'
+
+## Name the outfmp files
+echo  "bayer_macrocycles/ftase_extraligs_custcore_stereo/ftase_extraligs_custcore_stereo_out.fmp" > bayer_macrocycles_outs.txt
+echo "bayer_macrocycles/wagner_brd4/wagner_brd4_out.fmp" >>  bayer_macrocycles_outs.txt 
+
+#######################
+#FEP+ charge change set
+#######################
+echo 'Collecting FEP+ charge set data'
+
+## Apply the corrections
+cd charge_annhil
+./run_all_corrections.sh
+cd ../
+
+## Name the output fmp file locations
+PROTEINS=(cdk2 dlk egfr ephx2 irak4_s2 irak4_s3 itk jak1 jnk1 ptp1b tyk2)
+for P in ${PROTEINS[*]}
+do
+  echo "charge_annhil/${P}/${P}_pkacorr_out.fmp" >> charge_annhil_outs.txt
+done
+echo "charge_annhil/thrombin_whole_map/thrombin_whole_map_out.fmp" >> charge_annhil_outs.txt
+
+############
+# Fragements
+############
+echo 'Collecting fragement set data'
+
+cd fragments
+./run_all_corrections.sh
+cd ../
+
+PROTEINS=(frag_liga_auto frag_mcl1_noweak frag_mup1 frag_p38 hsp90_frag_2rings hsp90_frag_single_ring t4lysozyme_uvt)
+for P in ${PROTEINS[*]}
+do
+    echo "fragments/${P}/${P}_out.fmp" >> fragments_outs.txt
+done
+
+echo "fragments/jak2_set1/jak2_set1_pkacorr_bmcorr_out.fmp" >> fragments_outs.txt
+echo "fragments/jak2_set2_extra/jak2_set2_extra_bmcorr_out.fmp" >> fragments_outs.txt
+
+#######
+# GPCRs
+#######
+echo 'Collecting GPCR data'
+# Apply the corrections
+cd gpcrs
+./run_all_corrections.sh
+cd ../
+
+## Name the files
+echo "gpcrs/p2y1_merged_out.fmp" > gpcrs_outs.txt
+echo "gpcrs/a2a_hip278/a2a_hip278_sbpkacorr_out.fmp" >> gpcrs_outs.txt
+echo "gpcrs/ox2_hip_custcore/ox2_out.fmp" >> gpcrs_outs.txt
+
+#####################################
+# FEP+ R-group perutbation (JACS set)
+#####################################
+echo 'Collecting FEP+ R-group perutbation (JACS set) data'
+cd jacs_set/
+./run_all_corrections.sh
+cd ../
+
+echo "jacs_set/jnk1_manual_flips/jnk1_manual_flips_out_bmcorr_out.fmp" > jacs_set_outs.txt
+echo "jacs_set/mcl1_extra_flips/mcl1_extra_flips_bmcorr_out.fmp" >> jacs_set_outs.txt
+
+PROTEINS=(bace cdk2 jnk1_manual_flips mcl1_extra_flips p38 ptp1b thrombin_core tyk2)
+for P in ${PROTEINS[*]}
+do
+    echo "jacs_set/${P}/${P}_out.fmp" >> jacs_set_outs.txt
+done
+
+################
+# Janssen BACE1
+###############
+echo 'Collecting the Jansseen BACE1 data'
+
+cd janssen_bace 
+./run_all_corrections.sh
+cd ../
+
+echo "janssen_bace/bace_ciordia_retro/bace_ciordia_retro_pkacorr_out.fmp" > janssen_bace_outs.txt
+echo "janssen_bace/bace_keranen_p2/bace_keranen_p2_bmcorr_out.fmp" >> janssen_bace_outs.txt
+echo "janssen_bace/bace_ciordia_prospective/bace_ciordia_prospective_out.fmp" >> janssen_bace_outs.txt 
+echo "janssen_bace/bace_p3_arg368_in/bace_p3_arg368_in_out.fmp" >> janssen_bace_outs.txt
+
+##################
+# FEP+ Macrocycles
+##################
+echo 'Collecting FEP+ macrocycle data'
+PROTEINS=(2B8V_lig24and25_alpha05 2E9P_lig4to7_alpha05 2Q15_lig17to21_alpha05 3RKZ_lig62to70_alpha05 MHT1_lig3_alpha05 ck2_custcore_hotlys hsp90_3hvd_custcore)
+for P in ${PROTEINS[*]}
+do
+    echo "macrocycles/${P}/${P}_out.fmp" >> macrocycle_outs.txt
+done
+
+#############
+# MCS docking
+#############
+echo 'Collecting MCS docking data'
+cd mcs_docking
+./run_all_corrections.sh
+cd ../
+
+echo "mcs_docking/hne/hne_500mM_pkacorr_out.fmp" > mcs_docking_outs.txt
+echo "mcs_docking/renin_customcore/renin_customcore_out.fmp" >> mcs_docking_outs.txt
+
+#######
+# Merck
+######
+echo 'Collecting Merck data'
+cd  merck
+./run_all_corrections.sh
+cd ../
+
+echo 'merck/cdk8_5cei_new_helix_loop_extra/cdk8_symbmcorr_out.fmp' > merck_outs.txt
+echo 'merck/cmet/cmet_out.fmp' >> merck_outs.txt
+echo 'merck/eg5_extraprotomers/eg5_extraprotomers_pkacorr_out.fmp' >> merck_outs.txt
+echo 'merck/hif2a_automap/hif2a_automap_symbmcorr_out.fmp' >> merck_outs.txt
+#echo 'merck/pfkfb3_automap/pfkfb3_automap_symbmcorr_out_fmp' >> merck_outs.txt
+echo 'merck/shp2/shp2_out.fmp' >> merck_outs.txt
+echo 'merck/syk_4puz_fullmap/syk_pkacorr_out.fmp'  >> merck_outs.txt
+echo 'merck/tnks2_fullmap/tnks2_symcorr_pkacorr_out.fmp' >> merck_outs.txt
+
+###############
+# Miscellaneous
+###############
+echo 'Collecting the miscellaneous data sets'
+cd misc
+./run_all_corrections.sh
+cd ../
+
+PROTEINS=(cdk8_koehler galectin3_extra hfaah hiv_prot_ekegren)
+for P in ${PROTEINS[*]}
+do
+    echo "misc/${P}/${P}_out.fmp" >> misc_outs.txt
+done
+echo 'misc/btk_extra_flip/btk_extra_flip_bmcorr_out.fmp' >> misc_outs.txt
+
+######################
+# OPLS drug discovery
+#####################
+echo 'Collecting the OPLS drug discovery data sets'
+PROTEINS=(bathonP_ethers bathonP_thq bathonP_thq_ring hero0 hero1 hero3 hero5 iris lak1 lak2 lak3 orion)
+for P in ${PROTEINS[*]}
+do
+    echo "opls_ddag/${P}/${P}_out.fmp" >> opls_ddag_outs.txt
+done
+
+#############
+# OPLS Stress
+#############
+echo 'Collecting the OPLS stress set data'
+
+PROTEINS=(chk1_set1 chk1_set2 chk1_set3 chk1_set4 chk1_set5 chk1_set6 chk1_set7 cr_bace1 cr_bace2 fxa_set3 fxa_set4 fxa_set5 fxa_set6 hc_bace1 hc_bace2 pb_bace3 fxa_yoshikawa_set)
+for P in ${PROTEINS[*]}
+do
+    echo "opls_stress/${P}/${P}_out.fmp" >> opls_stress_outs.txt
+done
+
+###################
+# Scaffold hoppping
+###################
+echo 'Collecting the scaffold hopping data set'
+
+PROTEINS=(Bace1_4zsp CHK1_3u9n_corehop Era_2q70 Fxa_2ei8 TPSB2_3v7t)
+for P in ${PROTEINS[*]}
+do
+    echo "scaffold_hopping/${P}/${P}_out.fmp" >> scaffold_hopping_outs.txt
+done
+
+##########
+# Waterset
+##########
+echo 'Collecting the water displacement data set'
+
+cd waterset
+./run_all_corrections.sh
+cd ../
+
+PROTEINS=(hsp90_kung brd41_ASH106 taf12 urokinase hsp90_woodhead)
+for P in ${PROTEINS[*]}
+do
+   echo "waterset/${P}/${P}_out.fmp" >> waterset_outs.txt
+done
+echo 'waterset/scyt_dehyd/scyt_dehyd_pkacorr_out.fmp' >> waterset_outs.txt
+echo 'waterset/throm_nozob_hip75/throm_nozob_hip75_bmcorr_out.fmp' >> waterset_outs.txt
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/bayer_macrocycles/setup_and_run.sh b/fep_benchmark_inputs/fep_plus_inputs/bayer_macrocycles/setup_and_run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..d05a40c327a4031f9f89e302b09c9afa15edda79
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/bayer_macrocycles/setup_and_run.sh
@@ -0,0 +1,12 @@
+mkdir wagner_brd4
+cp wagner_brd4.fmp wagner_brd4
+cd wagner_brd4
+"${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME wagner_brd4 wagner_brd4.fmp -QARG "-P dev_GPU"
+cd ../
+
+mkdir ftase_extraligs_custcore_stereo
+cp ftase_extraligs_custcore_stereo.fmp ftase_extraligs_custcore_stereo
+cd ftase_extraligs_custcore_stereo
+"${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 40000.0 -vacuum -ensemble muVT -core_hopping_lambda_windows 48 -seed 1 -JOBNAME ftase_extraligs_custcore_stereo ftase_extraligs_custcore_stereo.fmp -QARG "-P dev_GPU"
+cd ../
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/bayer_macrocycles/subset_metadata.csv b/fep_benchmark_inputs/fep_plus_inputs/bayer_macrocycles/subset_metadata.csv
new file mode 100644
index 0000000000000000000000000000000000000000..1f0539d24222cb913fc2a13a750817e4af792c3d
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/bayer_macrocycles/subset_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c35be65c292d93a73caf0b697469c10be5ef8f49fa8f04bbc72701090ade620c
+size 335
diff --git a/fep_benchmark_inputs/fep_plus_inputs/binding_mode_correction.py b/fep_benchmark_inputs/fep_plus_inputs/binding_mode_correction.py
new file mode 100644
index 0000000000000000000000000000000000000000..d157dd66d086cceab5cda0449e46cea60aae24b7
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/binding_mode_correction.py
@@ -0,0 +1,242 @@
+import argparse
+import sys
+from collections import defaultdict
+from typing import List
+
+import numpy as np
+
+from schrodinger.application.desmond.constants import BOLTZMANN
+from schrodinger.application.desmond.measurement import Measurement
+from schrodinger.application.scisol.packages.fep import graph
+from schrodinger.structutils import analyze
+
+
+def clean_bennett_from_map(g: graph.Graph):
+    """
+    Removes the bennett complex and solvent free energy data and replace with the cycle closure correction DDG
+    predictions. This helps to simplify the application of the binding mode correction.
+
+    :param g: An FEP+ graph with output data.
+
+    Note
+    -----
+    The graph is modified in place.
+    """
+    # TODO: As this creates an inconsistency between the DDGs in the graph and the SID, the SID data is removed.
+    # The Jira ticket DESMOND-10777 has been raised to discuss the possibility of updating the SID in the future.
+    for e in g.edges_iter():
+        e.complex_dg = e.ccc_ddg
+        e.solvent_dg = Measurement(0, 0)
+        e.vacuum_dg = None
+        e.complex_sid = None
+        e.solvent_sid = None
+
+
+def get_binding_mode_nodes(g: graph.Graph) -> List[List[graph.Node]]:
+    """
+    Extract the nodes that represent different binding modes of the same
+    ligand. SMILES are used to identify which ligands are the same.
+
+    :param g: A graph that contains multiple binding modes of the ligands, with
+        each binding mode represented as a separate node.
+
+    :return: The nodes of the binding modes as a list of lists. Each entry in
+        the list contains all the nodes of the different binding modes of the
+        same ligand.
+    """
+    # Extract the unique SMILES of each node in the graph and place matching SMILES into the same dict entry
+    mode_nodes_dict = defaultdict(list)
+    for n in g.nodes_iter():
+        smile = analyze.generate_smiles(n.struc, unique=True)
+        mode_nodes_dict[smile].append(n)
+
+    # Return the nodes whose SMILES appear multiple times
+    return [val for val in mode_nodes_dict.values() if len(val) > 1]
+
+
+def calc_mode_corrections(mode_nodes: List[List[graph.Node]],
+                          temperature: float = 300.) -> List[np.ndarray]:
+    """
+    Calculate the binding mode correction for each mode and for each ligand.
+    The presence of other binding modes serves to increase the binding strength
+    of a ligands.
+
+    :param mode_nodes: A list of lists that contains the nodes of the different
+        binding modes of the same ligand.
+    :param temperature: The temperature of the simulation in Kelvin.
+
+    :returns: The binding mode corrections for each ligand. Each correction
+        accounts for the presence of the other nodes of the same ligand.
+    """
+    kT = BOLTZMANN * temperature
+    corrections = []
+    for nodes in mode_nodes:
+        dgs = np.array([n.pred_dg.val for n in nodes])
+        corrs = np.zeros(len(dgs))
+        for i in range(len(dgs)):
+            corrs[i] = -kT * np.log(np.sum(np.exp(-(dgs - dgs[i]) / kT)))
+        corrections.append(corrs)
+
+    return corrections
+
+
+def apply_corrections(mode_nodes: List[List[graph.Node]],
+                      corrections: List[np.ndarray]):
+    """
+    Apply the binding mode correction to each edge that is connected to a node that represents one of at least two
+    binding modes of the same ligand. The edge data are modified in place. and nothing is returned.
+
+    :param mode_nodes: A list of lists that contains the nodes of the different binding modes of the same ligand.
+    :param corrections: The binding mode corrections for each ligand.
+    """
+    for nodes, correction in zip(mode_nodes, corrections):
+        # There is a different correction for each binding mode of the same ligand.
+        for n, corr in zip(nodes, correction):
+            # Apply correction to every edge the node is part of.
+            for e in n.edges:
+                if n == e[0]:
+                    # Deduct the binding mode correction
+                    e.complex_dg -= Measurement(corr, 0)
+                else:
+                    # Add the correction
+                    e.complex_dg += Measurement(corr, 0)
+
+
+def correct_multiple_binding_modes(
+        g: graph.Graph) -> (List[List[graph.Node]], List[np.ndarray]):
+    """
+    Automatically detects different modes, calculates the free energy correction, and applies it to the map. The input
+    map is modified in place.
+
+    :param g: An FEP+ graph that contains multiple binding modes.
+
+    :returns mode_nodes: A list of lists that contains the nodes of the different binding modes of the same ligand.
+    :returns corrections: The binding mode corrections for each ligand.
+    """
+    # Simplify the map by replacing all the bennett DG information with the cycle closure corrected DGs
+    clean_bennett_from_map(g)
+    # Find which ligands have multiple binding modes using canonicalized SMILES:
+    mode_nodes = get_binding_mode_nodes(g)
+    # Calculate the binding mode corrections and apply to the map:
+    corrections = calc_mode_corrections(mode_nodes)
+    apply_corrections(mode_nodes, corrections)
+    g.calc_cycle_closure()
+
+    return mode_nodes, corrections
+
+
+def merge_ligand_nodes(g: graph.Graph, mode_nodes: List[List[graph.Node]],
+                       corrections: List[np.ndarray]):
+    """
+    Merge all nodes of different binding modes into a single one. The most
+    favourable binding mode of each ligand is retained. The graph is modified
+    in place.
+
+    :param g: An FEP+ graph that contains multiple binding modes. Cycle closure
+        must have called for the map for this function to run.
+    :param mode_nodes: A list of lists that contains the nodes of the different
+        binding modes of the same ligand.
+    :param corrections: The binding mode corrections for each ligand.
+    """
+    for n in g.nodes_iter():
+        if n.pred_dg is None:
+            raise ValueError('Cycle closure must be called for the input map.')
+
+    # Determine which nodes to keep and which nodes to discard.
+    # The mode that requires the least correction is the most favourable and it will be retained.
+    to_merge = []
+    to_keep = []
+    for c in corrections:
+        keep_ind = np.where(c == np.max(c))[0][0]
+        to_merge.append(np.where(c != c[keep_ind])[0])
+        to_keep.append(keep_ind)
+
+    # Add the edges of the binding modes into the one that will be retained.
+    nodes_to_delete = []
+    nodes_to_keep = []
+    for nodes, merge_inds, keep_inds in zip(mode_nodes, to_merge, to_keep):
+        for i in merge_inds:
+            # Add the neighbours of the other binding modes to the node that will be kept.
+            for n in nodes[i].neighbors:
+                g.add_edge(nodes[keep_inds], n)
+            nodes_to_delete.append(nodes[i])
+            nodes_to_keep.append(nodes[keep_inds])
+
+    # Looping through the nodes that will be kept, going through the edges, and adding the predicted binding data
+    for nodes in nodes_to_keep:
+        for e in nodes.edges:
+            n_initial, n_final = e.direction
+            e.complex_dg = n_final.pred_dg - n_initial.pred_dg
+            e.solvent_dg = Measurement(0, 0)
+            e.vacuum_dg = None
+
+    # Finally deleting the nodes of the duplicate binding modes.
+    g.remove_nodes_from(nodes_to_delete)
+
+    return nodes_to_keep
+
+
+def main(argv=None):
+    usage = """
+    Let map_out.fmp be an output from FEP+ that has different binding modes of some of the ligands. To
+    calculate the relative binding free between ligands in a way that accounts for the presence of multiple binding
+    modes, type
+
+    $SCHRODINGER/run -FROM scisol binding_mode_correction.py map_out.fmp -o map_bmcorr_out.fmp
+
+    By default, the output 'map_bmcorr_out.fmp' has nodes of the same ligand merged into one. Edges between merged nodes
+    do not have trajectory (fmpdb) information. To not merge the nodes, use the flag '-no-merge', like this
+
+    $SCHRODINGER/run -FROM scisol binding_mode_correction.py map_out.fmp -o map_bmcorr_out.fmp -no-merge
+    """
+    description = """
+    In FEP+, one can run maps that have different binding modes of ligands in different nodes. This script automatically
+    detects multiple binding modes in an FEP+ map and applies the binding mode correction to the calculated relative free
+    energies. When using this script, there are no limitations to the number of ligands and poses, or on the geometry of the map.
+
+    To aid visualization and MUE and RMSE calculation, nodes of the same ligand are automatically merged into a node
+    that represents the most favorable binding mode, although this feature can be switched off.
+
+    When applying the corrections, the Bennett DDGs are replaced with cycle closure corrected DDGs. As this creates an
+    inconsistency between the Bennett DDGs in the map and SID data, the SID data is removed from the map.
+    """
+    parser = argparse.ArgumentParser(usage=usage, description=description)
+    parser.add_argument(
+        'infile',
+        type=str,
+        help="The name of an out fmp file that contains multiple binding modes."
+    )
+    parser.add_argument(
+        '-o',
+        dest='outfile',
+        type=str,
+        help=
+        "The name of the output fmp file that has the binding mode correction for each edge, default='bmcorr_out.fmp'.",
+        default='bmcorr_out.fmp')
+    parser.add_argument(
+        '-no-merge',
+        action='store_true',
+        dest='no_merge',
+        help=
+        'Option to NOT merge nodes of the same binding mode into most favorable, default=False.',
+        default=False)
+    args = parser.parse_args(argv)
+
+    # Load the map that contains ligands with at least 2 binding modes:
+    g = graph.Graph.deserialize(args.infile)
+
+    if g.fep_type != graph.FEP_TYPES.SMALL_MOLECULE:
+        sys.exit("Only small molecule graphs are supported")
+
+    # Detect alternate binding modes and apply the correction:
+    mode_nodes, corrections = correct_multiple_binding_modes(g)
+
+    if not args.no_merge:
+        merge_ligand_nodes(g, mode_nodes, corrections)
+        g.calc_cycle_closure()
+
+    g.write(args.outfile)
+
+
+if __name__ == '__main__':
+    main()
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/cdk2_epikpka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/cdk2_epikpka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..698ed054c8455cf98ce70f0898bb1af21e661258
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/cdk2_epikpka.txt
@@ -0,0 +1,4 @@
+pH  7.5
+
+# ligand ligand pka
+39charg 39neu 4.60 
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/cdk2_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/cdk2_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d13eb405a3d34cfcbaa0331a520d3d2e444f85e
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/cdk2_pka.txt
@@ -0,0 +1,4 @@
+pH  7.5
+
+# ligand ligand pka
+39charg 39neu 3.23
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/dlk_epikpka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/dlk_epikpka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e800a4289d93836b8844ec12ad279dcb58094f77
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/dlk_epikpka.txt
@@ -0,0 +1,4 @@
+pH	7.5
+#Lig	pKa
+4neu 4charg     9.87	
+17neu 17charg	8.01
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/dlk_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/dlk_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65b861107c3c9af71f40c7ae29e45fc177a9e2f4
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/dlk_pka.txt
@@ -0,0 +1,4 @@
+pH	7.5
+#Lig	pKa
+4neu 4charg	9.34
+17neu 17charg	6.17
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/egfr_epikpka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/egfr_epikpka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a65765a5a7172fed05b904f0fcba1889a3c33ac8
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/egfr_epikpka.txt
@@ -0,0 +1,7 @@
+pH	7.5
+#Lig	pKa
+27neu 27chargR	8.54
+27neu 27chargS  8.54
+28neu 28charg	7.7
+29neu 29charg	9.15
+30neu 30charg	8.74
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/egfr_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/egfr_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68678af5f376b1d04108f7185f6438be42a93f78
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/egfr_pka.txt
@@ -0,0 +1,7 @@
+pH	7.5
+#Lig	pKa
+27neu 27chargR	8.25
+27neu 27chargS  8.30
+28neu 28charg	9.48
+29neu 29charg	8.61
+30neu 30charg	8.73
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/ephx2_epikpka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/ephx2_epikpka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d843da8128c12a1ef8ddbfdb70f3fad47b47ce1
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/ephx2_epikpka.txt
@@ -0,0 +1,4 @@
+pH	7.0
+#Lig	pKa
+19charg 19neu 4.43
+47charg 47neu 4.6
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/ephx2_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/ephx2_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8dd3f559807623942bf3c7f51195528d790ef6d
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/ephx2_pka.txt
@@ -0,0 +1,4 @@
+pH	7.0
+#Lig	pKa
+19charg 19neu 3.43
+47charg 47neu 3.25
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/irak4_s2_epikpka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/irak4_s2_epikpka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..183b4c538cfa2bdb2f09401ad3dc63cf05366826
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/irak4_s2_epikpka.txt
@@ -0,0 +1,4 @@
+pH	7.2
+#Lig	pKa
+5neu 5charg 8.43
+17neu 17charg 7.94
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/irak4_s2_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/irak4_s2_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..36ab5a53f6b175d8dbaa0f16c547d65af9adebb3
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/irak4_s2_pka.txt
@@ -0,0 +1,4 @@
+pH	7.2
+#Lig	pKa
+5neu 5charg 7.24
+17neu 17charg 7.67
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/irak4_s3_epikpka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/irak4_s3_epikpka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4adca133caa7a2f8c9a9e83e0460602a9507b40c
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/irak4_s3_epikpka.txt
@@ -0,0 +1,4 @@
+pH	7.2
+#Lig	pKa
+19neu 19charg 10.33
+28neu 28charg 11.14
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/irak4_s3_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/irak4_s3_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae761fdd0c6e845dea071962480182dbe22f5451
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/irak4_s3_pka.txt
@@ -0,0 +1,4 @@
+pH	7.2
+#Lig	pKa
+19neu 19charg 8.65
+28neu 28charg 8.5
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/itk_epikpka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/itk_epikpka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e3f27e4ed4b036b1ba254e89077b0d180ec5a1f7
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/itk_epikpka.txt
@@ -0,0 +1,3 @@
+pH	7.2
+#Lig	pKa
+1neu 1charg 9.01 
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/itk_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/itk_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6362caf821cb0194640b8cdfbc4bc91246967346
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/itk_pka.txt
@@ -0,0 +1,3 @@
+pH	7.2
+#Lig	pKa
+1neu 1charg 8.91
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/jak1_epikpka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/jak1_epikpka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..55b071e6e7fe5dd52212dfd374e538016519beae
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/jak1_epikpka.txt
@@ -0,0 +1,4 @@
+pH	7.2
+#Lig	pKa
+16neu 16charg 9.81
+18neu 18charg 8.67
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/jak1_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/jak1_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd8d2034dbfbf131abd40ee4586ce6bb20175834
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/jak1_pka.txt
@@ -0,0 +1,4 @@
+pH	7.2
+#Lig	pKa
+16neu 16charg 8.83
+18neu 18charg 6.25
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/jnk1_epikpka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/jnk1_epikpka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b1ab60c3cc5f746fcdd098f1765f13367be27f7d
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/jnk1_epikpka.txt
@@ -0,0 +1,4 @@
+pH	7.2
+#Lig	pKa
+19a_neu 19a_charg 8.38 
+19b_charg 19b_neu 4.25
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/jnk1_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/jnk1_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06f31914319f87a892c886ee51b6ce4d7860cfbf
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/jnk1_pka.txt
@@ -0,0 +1,4 @@
+pH	7.2
+#Lig	pKa
+19a_neu 19a_charg 9.46
+19b_charg 19b_neu 2.13
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/ptp1b_epikpka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/ptp1b_epikpka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc3bc786c27a939442d1d21c05b87e4950388503
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/ptp1b_epikpka.txt
@@ -0,0 +1,3 @@
+pH	7.0
+#Lig	pKa
+26neu 26charg 11.23 
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/ptp1b_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/ptp1b_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..676ab46c182528c5661e3e2bdc5435d2c7465045
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/ptp1b_pka.txt
@@ -0,0 +1,3 @@
+pH	7.0
+#Lig	pKa
+26neu 26charg 9.31
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/run_all_corrections.sh b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/run_all_corrections.sh
new file mode 100755
index 0000000000000000000000000000000000000000..a8b29d37d203565f7e9030c8aa779eb04344ecb0
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/run_all_corrections.sh
@@ -0,0 +1,8 @@
+PROTEINS=(cdk2 dlk egfr ephx2 irak4_s2 irak4_s3 itk jak1 jnk1 ptp1b tyk2)
+for P in ${PROTEINS[*]}
+do
+    cd "${P}"
+    $SCHRODINGER/run -FROM scisol pka_tautomer_correction.py "${P}"_out.fmp -pka-file ../"${P}"_pka.txt -o "${P}"_pkacorr_out.fmp    
+    cd ../
+done
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/setup_and_run.sh b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/setup_and_run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..4741a4e79249cd6c1df5a4bd2ea274b7665776cd
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/setup_and_run.sh
@@ -0,0 +1,10 @@
+PROTEINS=(cdk2 dlk egfr ephx2 irak4_s2 irak4_s3 itk jak1 jnk1 ptp1b thrombin_whole_map tyk2)
+for P in ${PROTEINS[*]}
+do
+    mkdir "${P}"
+    cp ${P}.fmp ${P}
+    cd "${P}"
+    "${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME ${P} ${P}.fmp -QARG "-P dev_GPU"
+    cd ../
+done
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/subset_metadata.csv b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/subset_metadata.csv
new file mode 100644
index 0000000000000000000000000000000000000000..7d919e445520f0d96a7c442fbb993e6d9c3bfb57
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/subset_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:366d46ca0a92d6c91ca1182571cfe156d4c8c4a2024fb78f49fe7e2bbdf02442
+size 1072
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/tyk2_epikpka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/tyk2_epikpka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1adc49c67d6f07f15675eeb2d3232c94ca79a6dd
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/tyk2_epikpka.txt
@@ -0,0 +1,4 @@
+pH	7.0
+#Lig	pKa
+jmc_3charg jmc_32neu 4.53
+ejm_52neu ejm_52charg 8.80
diff --git a/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/tyk2_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/tyk2_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..537e64f3b11e62bf62adcf60e65e2e0bd825a4fb
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/charge_annhil/tyk2_pka.txt
@@ -0,0 +1,4 @@
+pH	7.0
+#Lig	pKa
+jmc_3charg jmc_32neu 3.52
+ejm_52neu ejm_52charg 9.36
diff --git a/fep_benchmark_inputs/fep_plus_inputs/fragments/jak2_set1_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/fragments/jak2_set1_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ccd3bde73be4bef7d4be0d4e6d6e3988d7741e1
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/fragments/jak2_set1_pka.txt
@@ -0,0 +1,4 @@
+pH  7.0
+
+# ligand ligand percent percent   
+4a 4b 0.5 0.5
diff --git a/fep_benchmark_inputs/fep_plus_inputs/fragments/run_all_corrections.sh b/fep_benchmark_inputs/fep_plus_inputs/fragments/run_all_corrections.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5be6af0df5d17c868c4c9d1113c201492db73095
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/fragments/run_all_corrections.sh
@@ -0,0 +1,11 @@
+cp jak2_set1_pka.txt run_jak2_set1_corrs.sh jak2_set1
+cd jak2_set1
+./run_jak2_set1_corrs.sh
+cd ../
+
+cd jak2_set2_extra
+cp ../run_jak2_set2_corrs.sh .
+./run_jak2_set2_corrs.sh
+rm run_jak2_set2_corrs.sh
+cd ../
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/fragments/run_jak2_set1_corrs.sh b/fep_benchmark_inputs/fep_plus_inputs/fragments/run_jak2_set1_corrs.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ecebda31779a5e4d2f97f8095279dad67cfaac80
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/fragments/run_jak2_set1_corrs.sh
@@ -0,0 +1,3 @@
+$SCHRODINGER/run -FROM scisol pka_tautomer_correction.py jak2_set1_out.fmp -p jak2_set1_pka.txt -o jak2_set1_pkacorr_out.fmp
+$SCHRODINGER/run -FROM scisol binding_mode_correction.py jak2_set1_pkacorr_out.fmp -o jak2_set1_pkacorr_bmcorr_out.fmp
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/fragments/run_jak2_set2_corrs.sh b/fep_benchmark_inputs/fep_plus_inputs/fragments/run_jak2_set2_corrs.sh
new file mode 100755
index 0000000000000000000000000000000000000000..8c7c1d017518fe535ea7ca228766ca83d120db08
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/fragments/run_jak2_set2_corrs.sh
@@ -0,0 +1,2 @@
+$SCHRODINGER/run -FROM scisol binding_mode_correction.py jak2_set2_extra_out.fmp -o jak2_set2_extra_bmcorr_out.fmp
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/fragments/setup_and_run.sh b/fep_benchmark_inputs/fep_plus_inputs/fragments/setup_and_run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..382c9ff9c352c5c170c9601530eeb635326a0c34
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/fragments/setup_and_run.sh
@@ -0,0 +1,10 @@
+PROTEINS=(frag_liga_auto frag_mcl1_noweak frag_mup1 frag_p38 hsp90_frag_2rings hsp90_frag_single_ring jak2_set1 jak2_set2_extra t4lysozyme_uvt)
+for P in ${PROTEINS[*]}
+do
+    mkdir "${P}"
+    cp ${P}.fmp ${P}
+    cd "${P}"
+    "${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME ${P} ${P}.fmp -QARG "-P dev_GPU"
+    cd ../
+done
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/fragments/subset_metadata.csv b/fep_benchmark_inputs/fep_plus_inputs/fragments/subset_metadata.csv
new file mode 100644
index 0000000000000000000000000000000000000000..1db03cd2f313843d8111d6bac486bab7fb3527c0
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/fragments/subset_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:53f0c1b87248e0a7896f0e6f79577f696d027fd186aab6eb5165cb638c329bd7
+size 908
diff --git a/fep_benchmark_inputs/fep_plus_inputs/gpcrs/a2a_epik_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/gpcrs/a2a_epik_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20bbf50456fc8b0427ef3470286024cab7b6f0a3
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/gpcrs/a2a_epik_pka.txt
@@ -0,0 +1,6 @@
+pH 7.5
+
+4o_4o deprotonated_9.84
+4e D_4eD deprotonated_8.43
+4e U 4eu deprotonated_8.43
+4f_4f deprotonated_10.72
diff --git a/fep_benchmark_inputs/fep_plus_inputs/gpcrs/a2a_symbmcorr.py b/fep_benchmark_inputs/fep_plus_inputs/gpcrs/a2a_symbmcorr.py
new file mode 100644
index 0000000000000000000000000000000000000000..91ce61b0a3b745876b1754c7ce4052cb7de6b1c6
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/gpcrs/a2a_symbmcorr.py
@@ -0,0 +1,99 @@
+from schrodinger.application.scisol.packages.fep import graph
+import numpy as np
+import argparse
+
+import sys
+sys.path.append('../')
+import binding_mode_correction as bmc
+
+# Add the symmetry corrections
+degree_of_symm = {'4a':4, '4a flipped':4,
+             '4b D':2,
+             '4b U':2,
+             '4c':4,
+             '4d':4,
+             '4e D':2, '4eD deprotonated':2,
+             '4e U':2, '4eU deprotonated':2,
+             '4f':4, '4f deprotonated':4,
+             '4g':4,
+             '4h':4,
+             '4i':4,
+             '4jR':2,
+             '4jS':2,
+             '4kD':2,
+             '4kU':2,
+             '4lD':2,
+             '4lU':2,
+             '4m D':2,
+             '4m U':2,
+             '4n':4,
+             '4o':4, '4o deprotonated':4,
+             '4q':4,
+             '4r D':2,
+             '4r U':2}
+
+def get_lignames(edge):
+    sep = edge.short_id_title.split('==>')
+    lig1 = sep[0].split(':')[1].strip()
+    lig2 = sep[1].split(':')[1].strip()
+    return lig1, lig2
+
+
+
+def main(argv=None):
+    usage="""
+    Apply the symmetry and binding mode correction to a particular map.
+
+    $SCHRODINGER/run symbmcorr.py map_out.fmp -o map_bmcorr_out.fmp
+    """
+    parser = argparse.ArgumentParser(usage=usage)
+    parser.add_argument('infile',
+                        type=str,
+                        help="The name of an out fmp file that contains multiple binding modes.")
+    parser.add_argument('-o',
+                        dest='outfile',
+                        type=str,
+                        help="If entered, the name of the corrected map, default=None.",
+                        default=None)
+    args = parser.parse_args(argv)
+
+
+    g = graph.Graph.deserialize(args.infile)
+
+    # Remove edges if they don't have predictions:
+    remove_edges = []
+    for e in g.edges_iter():
+        if e.complex_dg is None or e.solvent_dg is None:
+            remove_edges.append(e)
+
+    if len(remove_edges) > 0:
+        print('Removing {} edges as they do not have results'.format(len(remove_edges)))
+        g.remove_edges_from(remove_edges)
+
+    remove_nodes = []
+    for n in g.nodes_iter():
+        if n.pred_dg is None:
+            remove_nodes.append(n)
+
+    if len(remove_nodes) > 0:
+        print('Removing {} nodes as they do not have results'.format(len(remove_nodes)))
+        g.remove_nodes_from(remove_nodes)
+
+    kT =0.596
+    for e in g.edges_iter():
+        l1, l2 = get_lignames(e)
+        total_corr = 0
+        # Symmetry correction
+        total_corr += kT * np.log(degree_of_symm[l1])
+        total_corr -= kT * np.log(degree_of_symm[l2])
+        e.complex_dg += total_corr
+
+    g.calc_cycle_closure()
+
+    mode_nodes, corrections = bmc.correct_multiple_binding_modes(g)
+    bmc.merge_ligand_nodes(g, mode_nodes, corrections)
+    g.calc_cycle_closure()
+    g.write(args.outfile)
+
+if __name__ == '__main__':
+    main()
diff --git a/fep_benchmark_inputs/fep_plus_inputs/gpcrs/run_a2a_corrs.sh b/fep_benchmark_inputs/fep_plus_inputs/gpcrs/run_a2a_corrs.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f2ad9c6addb5cca958f74f3672265725dd9848bb
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/gpcrs/run_a2a_corrs.sh
@@ -0,0 +1,3 @@
+$SCHRODINGER/run a2a_symbmcorr.py a2a_hip278/a2a_hip278_out.fmp -o a2a_hip278/a2a_hip278_symbmcorr_out.fmp
+$SCHRODINGER/run -FROM scisol pka_tautomer_correction.py a2a_hip278/a2a_hip278_symbmcorr_out.fmp -o a2a_hip278/a2a_hip278_sbpkacorr_out.fmp -s_ -pka-file a2a_epik_pka.txt
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/gpcrs/run_all_corrections.sh b/fep_benchmark_inputs/fep_plus_inputs/gpcrs/run_all_corrections.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9510707627afaff49e335395f5abc7ac22e7ae12
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/gpcrs/run_all_corrections.sh
@@ -0,0 +1,3 @@
+./run_a2a_corrs.sh 
+$SCHRODINGER/run -FROM scisol merge_graph.py p2y1_meta_sub/p2y1_meta_sub_out.fmp p2y1_ortho_sub/p2y1_ortho_sub_out.fmp -o p2y1_merged_out.fmp -sc
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/gpcrs/setup_and_run.sh b/fep_benchmark_inputs/fep_plus_inputs/gpcrs/setup_and_run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..c393df95bbe2060be6c6d0a418e2c6ac0e99e5af
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/gpcrs/setup_and_run.sh
@@ -0,0 +1,15 @@
+PROTEINS=(a2a_hip278 p2y1_meta_sub p2y1_ortho_sub)
+for P in ${PROTEINS[*]}
+do
+    mkdir "${P}"
+    cp ${P}.fmp ${P}
+    cd "${P}"
+    "${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME ${P} ${P}.fmp -QARG "-P dev_GPU"
+    cd ../
+done
+
+mkdir ox2_hip_custcore
+cp ox2_hip_custcore.fmp ox2_hip_custcore
+cd ox2_hip_custcore
+"${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -vacuum -modify_dihe -ensemble muVT -seed 1 -JOBNAME ox2 ox2_hip_custcore.fmp -QARG "-P dev_GPU"
+cd ../
diff --git a/fep_benchmark_inputs/fep_plus_inputs/gpcrs/subset_metadata.csv b/fep_benchmark_inputs/fep_plus_inputs/gpcrs/subset_metadata.csv
new file mode 100644
index 0000000000000000000000000000000000000000..e7c1e0e990233d339b6c2af10884b791257d1666
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/gpcrs/subset_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9313a9f142f12eea9556462a94c83da9d1f9c7bc9f229471490419255f8ab5e5
+size 419
diff --git a/fep_benchmark_inputs/fep_plus_inputs/jacs_set/run_all_corrections.sh b/fep_benchmark_inputs/fep_plus_inputs/jacs_set/run_all_corrections.sh
new file mode 100755
index 0000000000000000000000000000000000000000..8687203eb26d67da49be0f603dad081be8ae86d2
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/jacs_set/run_all_corrections.sh
@@ -0,0 +1,2 @@
+$SCHRODINGER/run -FROM scisol binding_mode_correction.py jnk1_manual_flips/jnk1_manual_flips_out.fmp -o jnk1_manual_flips/jnk1_manual_flips_out_bmcorr_out.fmp
+$SCHRODINGER/run -FROM scisol binding_mode_correction.py mcl1_extra_flips/mcl1_extra_flips_out.fmp -o mcl1_extra_flips/mcl1_extra_flips_bmcorr_out.fmp
diff --git a/fep_benchmark_inputs/fep_plus_inputs/jacs_set/setup_and_run.sh b/fep_benchmark_inputs/fep_plus_inputs/jacs_set/setup_and_run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..48b21a5fd429bd6f08e5e51b9173555c0db61e05
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/jacs_set/setup_and_run.sh
@@ -0,0 +1,9 @@
+PROTEINS=(bace cdk2 jnk1_manual_flips mcl1_extra_flips p38 ptp1b thrombin_core tyk2)
+for P in ${PROTEINS[*]}
+do
+    mkdir "${P}"
+    cp ${P}.fmp ${P}
+    cd "${P}"
+    "${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME ${P} ${P}.fmp -QARG "-P dev_GPU"
+    cd ../
+done
diff --git a/fep_benchmark_inputs/fep_plus_inputs/jacs_set/subset_metadata.csv b/fep_benchmark_inputs/fep_plus_inputs/jacs_set/subset_metadata.csv
new file mode 100644
index 0000000000000000000000000000000000000000..77a0f47d844e2c3a54a42a96d820f67271145bb5
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/jacs_set/subset_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:512de45d69255c67939d04439d00582c827e2d195a112abc52eb304ad29de8ed
+size 731
diff --git a/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/bace_ciordia_retro_symbmcorr.py b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/bace_ciordia_retro_symbmcorr.py
new file mode 100644
index 0000000000000000000000000000000000000000..386840c2501b1b5ddcdb7a5bfdcab38a254e208d
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/bace_ciordia_retro_symbmcorr.py
@@ -0,0 +1,100 @@
+from schrodinger.application.scisol.packages.fep import graph
+import numpy as np
+import argparse
+from itertools import combinations
+
+import sys
+sys.path.append('/home/ross/Work/schrython/')
+import fep_tools as ftools
+import binding_mode_correction as bmc
+
+
+def get_lignames(edge):
+    sep = edge.short_id_title.split('==>')
+    lig1 = sep[0].split(':')[1].strip()
+    lig2 = sep[1].split(':')[1].strip()
+    return lig1, lig2
+
+
+# Add the symmetry corrections. Specific to the map
+degree_of_symm = {'17':2}
+
+def get_error_before_corrs(g):
+    pred_dgs = []
+    exp_dgs = []
+    for n in g.nodes_iter():
+        ligname = n.short_id_title.split(":")[1].strip()
+        if 'flip' not in ligname:
+            pred_dgs.append(n.pred_dg.val)
+            exp_dgs.append(n.exp_dg.val)
+
+    pred_dgs = np.array(pred_dgs)
+    exp_dgs = np.array(exp_dgs)
+
+    pred_dgs += np.mean(exp_dgs) - np.mean(pred_dgs)
+
+    indices = np.arange(len(exp_dgs))
+    pred_pairwise = np.array([pred_dgs[i] - pred_dgs[j] for i, j in combinations(indices, 2)])
+    exp_pairwise = np.array([exp_dgs[i] - exp_dgs[j] for i, j in combinations(indices, 2)])
+
+    sq_diffs = (exp_pairwise - pred_pairwise)**2
+    boot_rmsds = np.zeros(10000)
+    for b in range(10000):
+        samp_inds = np.random.choice(len(sq_diffs), len(sq_diffs))
+        arr_boot = sq_diffs[samp_inds]
+        boot_rmsds[b] = np.sqrt(arr_boot.mean())
+
+    pair_rmsd = np.sqrt(np.mean((exp_pairwise - pred_pairwise)**2))
+    print('Pairwise RMSD without extra rotamers and symmetry correction = {:.2f} +/- {:.2f} kcal/mol'.format(pair_rmsd, np.std(boot_rmsds)))
+
+
+def main(argv=None):
+    usage="""
+    Apply the symmetry and binding mode correction to a particular map.
+
+    $SCHRODINGER/run symbmcorr.py map_out.fmp -o map_bmcorr_out.fmp
+    """
+    parser = argparse.ArgumentParser(usage=usage)
+    parser.add_argument('infile',
+                        type=str,
+                        help="The name of an out fmp file that contains multiple binding modes.")
+    parser.add_argument('-o',
+                        dest='outfile',
+                        type=str,
+                        help="If entered, the name of the corrected map, default=None.",
+                        default=None)
+    args = parser.parse_args(argv)
+
+    g = graph.Graph.deserialize(args.infile)
+
+    ftools.pretty_print_fmp(g)
+    print()
+    print(get_error_before_corrs(g))
+    print()
+
+    # SYMMETRY CORRECTION
+    kT =0.596
+    for e in g.edges_iter():
+        l1, l2 = get_lignames(e)
+        total_corr = 0
+        # Symmetry correction
+        if l1 in degree_of_symm:
+            total_corr += kT * np.log(degree_of_symm[l1])
+        if l2 in degree_of_symm:
+            total_corr -= kT * np.log(degree_of_symm[l2])
+        e.complex_dg += total_corr
+
+    g.calc_cycle_closure()
+
+    # BINDING MODE CORRECTION
+    mode_nodes, corrections = bmc.correct_multiple_binding_modes(g)
+    bmc.merge_ligand_nodes(g, mode_nodes, corrections)
+    g.calc_cycle_closure()
+
+    ftools.pretty_print_fmp(g)
+
+    if args.outfile is not None:
+        g.write(args.outfile)
+
+if __name__ == '__main__':
+    main()
diff --git a/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/bace_retrospective_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/bace_retrospective_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ab2ba83f616d0fadf70d3f1f551c05edfa9747e
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/bace_retrospective_pka.txt
@@ -0,0 +1,4 @@
+pH  4.5
+
+# ligand ligand  pka
+30 30_protonated 6.45 
diff --git a/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/run_all_corrections.py b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/run_all_corrections.py
new file mode 100755
index 0000000000000000000000000000000000000000..8a0be09280d95cd0f1b3095dfc7d73b6e95583a1
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/run_all_corrections.py
@@ -0,0 +1,2 @@
+./run_bace_ciordia_retro_corrs.sh
+./run_bace_keranen_p2_corrs.sh
diff --git a/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/run_bace_ciordia_retro_corrs.sh b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/run_bace_ciordia_retro_corrs.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5727c5a32533d54b6cf6be4f20b0e233f439e602
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/run_bace_ciordia_retro_corrs.sh
@@ -0,0 +1 @@
+$SCHRODINGER/run -FROM scisol pka_tautomer_correction.py bace_ciordia_retro/bace_ciordia_retro_out.fmp -pka-file bace_retrospective_pka.txt -o bace_ciordia_retro/bace_ciordia_retro_pkacorr_out.fmp 
diff --git a/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/run_bace_keranen_p2_corrs.sh b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/run_bace_keranen_p2_corrs.sh
new file mode 100755
index 0000000000000000000000000000000000000000..597fcef329010f758c948b73961222db67b10922
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/run_bace_keranen_p2_corrs.sh
@@ -0,0 +1 @@
+$SCHRODINGER/run -FROM scisol binding_mode_correction.py bace_keranen_p2/bace_keranen_p2_out.fmp -o bace_keranen_p2/bace_keranen_p2_bmcorr_out.fmp
diff --git a/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/setup_and_run.sh b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/setup_and_run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..6a742c2de847468008fab00f089b3c3ec980bc38
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/setup_and_run.sh
@@ -0,0 +1,15 @@
+PROTEINS=(bace_ciordia_prospective bace_ciordia_retro bace_keranen_p2)
+for P in ${PROTEINS[*]}
+do
+    mkdir "${P}"
+    cp ${P}.fmp ${P}
+    cd "${P}"
+    "${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME ${P} ${P}.fmp -QARG "-P dev_GPU"
+    cd ../
+done
+
+mkdir bace_p3_arg368_in
+cp bace_p3_arg368_in.fmp bace_p3_arg368_in
+cd bace_p3_arg368_in
+"${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -core-hopping-lambda-windows 32 -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME bace_p3 bace_p3_arg368_in.fmp -QARG "-P dev_GPU"
+cd ..
diff --git a/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/subset_metadata.csv b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/subset_metadata.csv
new file mode 100644
index 0000000000000000000000000000000000000000..3c48ced8cbfb9eeac40eb61dcaab155cee46fd18
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/janssen_bace/subset_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e9b2be5e275f8f72a052ccca2c1cd04159669ee99059abf21b926933b7063921
+size 505
diff --git a/fep_benchmark_inputs/fep_plus_inputs/macrocycles/setup_and_run.sh b/fep_benchmark_inputs/fep_plus_inputs/macrocycles/setup_and_run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..a15dd5db01e45bc00211ad1ed4824e6a899df0fc
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/macrocycles/setup_and_run.sh
@@ -0,0 +1,19 @@
+PROTEINS=(2B8V_lig24and25_alpha05 2E9P_lig4to7_alpha05 2Q15_lig17to21_alpha05 3RKZ_lig62to70_alpha05 MHT1_lig3_alpha05)
+for P in ${PROTEINS[*]}
+do
+    mkdir "${P}"
+    cp ${P}.fmp ${P}
+    cd "${P}"
+    "${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME ${P} ${P}.fmp -QARG "-P dev_GPU"
+    cd ../
+done
+
+PROTEINS=(ck2_custcore_hotlys hsp90_3hvd_custcore)
+for P in ${PROTEINS[*]}
+do
+    mkdir "${P}"
+    cp ${P}.fmp ${P}
+    cd "${P}"
+    "${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -modify_dihe -vacuum -ensemble muVT -seed 1 -JOBNAME ${P} ${P}.fmp -QARG "-P dev_GPU"
+    cd ../
+done
diff --git a/fep_benchmark_inputs/fep_plus_inputs/macrocycles/subset_metadata.csv b/fep_benchmark_inputs/fep_plus_inputs/macrocycles/subset_metadata.csv
new file mode 100644
index 0000000000000000000000000000000000000000..07f763f232f3048b9c130f3e52d988caf84ccf05
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/macrocycles/subset_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7399823b4a570f234d7a23cfc1354e75355444dbae7074af2338ed0796a1652e
+size 803
diff --git a/fep_benchmark_inputs/fep_plus_inputs/mcs_docking/hne_epik_pka.txt b/fep_benchmark_inputs/fep_plus_inputs/mcs_docking/hne_epik_pka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aca51bd3260ce52bcc30376e4e5313e3388a8445
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/mcs_docking/hne_epik_pka.txt
@@ -0,0 +1,7 @@
+pH  7.4
+
+# ligand     ligand      pka
+21 neutral_21_8.53
+21 (SP core01) neutral_21 (SP core01)_8.83
+16 neutral_16_3.58
+19 neutral_19_3.66
diff --git a/fep_benchmark_inputs/fep_plus_inputs/mcs_docking/run_all_corrections.sh b/fep_benchmark_inputs/fep_plus_inputs/mcs_docking/run_all_corrections.sh
new file mode 100755
index 0000000000000000000000000000000000000000..0ac01049ee5a1ab9e1ededa561c3515c59d4ec33
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/mcs_docking/run_all_corrections.sh
@@ -0,0 +1,2 @@
+$SCHRODINGER/run -FROM scisol pka_tautomer_correction.py hne/hne_500mM_out.fmp -pka-file hne_epik_pka.txt -o hne/hne_500mM_pkacorr_out.fmp -s_
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/mcs_docking/setup_and_run.sh b/fep_benchmark_inputs/fep_plus_inputs/mcs_docking/setup_and_run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..20776b89142bb0e4d49242c14614677d3d6acaa0
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/mcs_docking/setup_and_run.sh
@@ -0,0 +1,12 @@
+
+mkdir renin_customcore
+cp renin_customcore.fmp renin_customcore
+cd renin_customcore
+"${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ffbuilder -ff-host bolt_cpu:50 -ppj 2 -time 20000.0 -ensemble muVT -seed 1 -vacuum -lambda_windows 12 -core_hopping_lambda_windows 16 -charged_lambda_windows 24 -JOBNAME renin_customcore renin_customcore.fmp -TMPLAUNCHDIR -QARG "-P dev_GPU" -modify-dihe
+cd ../
+
+mkdir hne
+cp hne.fmp hne
+cd hne
+"${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ffbuilder -ff-host bolt_cpu:50 -ppj 2 -time 20000.0 -ensemble muVT -salt 0.5 -seed 1 -vacuum -lambda_windows 12 -core_hopping_lambda_windows 16 -charged_lambda_windows 24 -JOBNAME hne_500mM hne.fmp -TMPLAUNCHDIR  -QARG "-P dev_GPU"
+cd ../ 
diff --git a/fep_benchmark_inputs/fep_plus_inputs/mcs_docking/subset_metadata.csv b/fep_benchmark_inputs/fep_plus_inputs/mcs_docking/subset_metadata.csv
new file mode 100644
index 0000000000000000000000000000000000000000..63c7793fcb12e4042bef57bfd620475c1dabcaf5
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/mcs_docking/subset_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3aca55145c5f6b51430fe7854d0edea9d56f2e64c10e5e20279992b64803b85b
+size 293
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/cdk8_symbmcorr.py b/fep_benchmark_inputs/fep_plus_inputs/merck/cdk8_symbmcorr.py
new file mode 100644
index 0000000000000000000000000000000000000000..592162ac9830a2cb436681a62c8b1f7c98d29748
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/cdk8_symbmcorr.py
@@ -0,0 +1,133 @@
+from schrodinger.application.scisol.packages.fep import graph
+import numpy as np
+import argparse
+from itertools import combinations
+
+
+import sys
+sys.path.append('../')
+import binding_mode_correction as bmc
+
+
+def get_lignames(edge):
+    sep = edge.short_id_title.split('==>')
+    lig1 = sep[0].split(':')[1].strip()
+    lig2 = sep[1].split(':')[1].strip()
+    return lig1, lig2
+
+def get_pairwise_diffs(g):
+    pred_dg = np.zeros(len(g))
+    exp_dg = np.zeros(len(g))
+    for i, n in enumerate(g.nodes_iter()):
+        pred_dg[i] = n.pred_dg
+        exp_dg[i] = n.exp_dg
+
+    #print('Error before', np.mean(np.abs(pred_dg - exp_dg)))
+    # Make sure the predictions are centered on the experimental dgs
+    pred_dg += np.mean(exp_dg) - np.mean(pred_dg)
+    #print('Error after', np.mean(np.abs(pred_dg - exp_dg)))
+
+    indices = np.arange(len(g))
+    pred_pairwise = np.array([pred_dg[i] - pred_dg[j] for i, j in combinations(indices, 2)])
+    exp_pairwise = np.array([exp_dg[i] - exp_dg[j] for i, j in combinations(indices, 2)])
+
+    return exp_pairwise, pred_pairwise
+
+
+def get_error_before_corrs(g):
+    pred_dgs = []
+    exp_dgs = []
+    for n in g.nodes_iter():
+        ligname = n.short_id_title.split(":")[1].strip()
+        if 'flipped' not in ligname:
+            pred_dgs.append(n.pred_dg.val)
+            exp_dgs.append(n.exp_dg.val)
+
+    pred_dgs = np.array(pred_dgs)
+    exp_dgs = np.array(exp_dgs)
+
+    pred_dgs += np.mean(exp_dgs) - np.mean(pred_dgs)
+
+    indices = np.arange(len(exp_dgs))
+    pred_pairwise = np.array([pred_dgs[i] - pred_dgs[j] for i, j in combinations(indices, 2)])
+    exp_pairwise = np.array([exp_dgs[i] - exp_dgs[j] for i, j in combinations(indices, 2)])
+
+    sq_diffs = (exp_pairwise - pred_pairwise)**2
+    boot_rmsds = np.zeros(10000)
+    for b in range(10000):
+        samp_inds = np.random.choice(len(sq_diffs), len(sq_diffs))
+        arr_boot = sq_diffs[samp_inds]
+        boot_rmsds[b] = np.sqrt(arr_boot.mean())
+
+    pair_rmsd = np.sqrt(np.mean((exp_pairwise - pred_pairwise)**2))
+    #print('Pairwise RMSD without extra rotamers and symmetry correction = {:.2f} +/- {:.2f} kcal/mol'.format(pair_rmsd, np.std(boot_rmsds)))
+
+
+# Add the symmetry corrections. Specific to the map
+no_sym_corr = ['13','13 flipped', '14', '15', '16', '16 flipped','17', '17 flipped', '18', '18 flipped', '42','43','43 flipped', '44', '44 flipped', '45','45 flipped']
+
+def main(argv=None):
+    usage="""
+    Apply the symmetry and binding mode correction to a particular map.
+
+    $SCHRODINGER/run symbmcorr.py map_out.fmp -o map_bmcorr_out.fmp
+    """
+    parser = argparse.ArgumentParser(usage=usage)
+    parser.add_argument('infile',
+                        type=str,
+                        help="The name of an out fmp file that contains multiple binding modes.")
+    parser.add_argument('-o',
+                        dest='outfile',
+                        type=str,
+                        help="If entered, the name of the corrected map, default=None.",
+                        default=None)
+    args = parser.parse_args(argv)
+
+    g = graph.Graph.deserialize(args.infile)
+
+    get_error_before_corrs(g)
+
+    # Remove edges if they don't have predictions:
+    remove_edges = []
+    for e in g.edges_iter():
+        if e.complex_dg is None or e.solvent_dg is None:
+            remove_edges.append(e)
+    
+    if len(remove_edges) > 0:
+        #print('Removing {} edges as they do not have results'.format(len(remove_edges))) 
+        g.remove_edges_from(remove_edges) 
+
+    remove_nodes = []
+    for n in g.nodes_iter():
+        if n.pred_dg is None:
+            remove_nodes.append(n)
+    
+    if len(remove_nodes) > 0:
+        #print('Removing {} nodes as they do not have results'.format(len(remove_nodes)))
+        g.remove_nodes_from(remove_nodes)
+
+
+    # SYMMETRY CORRECTION
+    kT =0.596
+    for e in g.edges_iter():
+        l1, l2 = get_lignames(e)
+        total_corr = 0
+        # Symmetry correction
+        if l1 not in no_sym_corr:
+            total_corr += kT * np.log(2)
+        if l2 not in no_sym_corr:
+            total_corr -= kT * np.log(2)
+        e.complex_dg += total_corr
+
+    g.calc_cycle_closure()
+
+    # BINDING MODE CORRECTION
+    mode_nodes, corrections = bmc.correct_multiple_binding_modes(g)
+    bmc.merge_ligand_nodes(g, mode_nodes, corrections)
+    g.calc_cycle_closure()
+
+    if args.outfile is not None:
+        g.write(args.outfile)
+
+if __name__ == '__main__':
+    main()
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/eg5_populations_epik.txt b/fep_benchmark_inputs/fep_plus_inputs/merck/eg5_populations_epik.txt
new file mode 100644
index 0000000000000000000000000000000000000000..913e186bdcc0f0294a8a63d9da2ade4d265dc2f2
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/eg5_populations_epik.txt
@@ -0,0 +1,6 @@
+CHEMBL1084935-CHEMBL1084935_1-0.9078154298419999-0.09218457015800006
+CHEMBL1096002-CHEMBL1096002_1-0.9853087750803547-0.014691224919645345
+CHEMBL1084677-CHEMBL1084677_1-0.9952314810830681-0.004768518916931795
+CHEMBL1096003-CHEMBL1096003_1-0.9513853050845874-0.04861469491541258
+CHEMBL1084143-CHEMBL1084143_1-0.9944008756500452-0.005599124349954684
+CHEMBL1084676-CHEMBL1084676_1-0.9784218934304049-0.021578106569595093
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/extract_epik_pop_corrs.py b/fep_benchmark_inputs/fep_plus_inputs/merck/extract_epik_pop_corrs.py
new file mode 100644
index 0000000000000000000000000000000000000000..cba1352d3a148810ced018ceb59d2174808f5974
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/extract_epik_pop_corrs.py
@@ -0,0 +1,82 @@
+import numpy as np
+from schrodinger.application.scisol.packages.fep.graph import Graph
+import argparse
+from collections import defaultdict
+
+epik_penalty_names = ('r_epik_Ionization_Penalty',
+                      'r_epik_Ionization_Penalty_Charging',
+                      'r_epik_Ionization_Penalty_Neutral',
+                      'r_epik_State_Penalty',
+                      'r_epik_Charging_Adjusted_Penalty',
+                      'i_epik_Tot_Q',
+                      'i_epik_Tot_abs_Q',
+                      'r_lp_tautomer_probability')
+ 
+def extract_supernodes(g):
+    smile2node = defaultdict(list)
+    for n in g.nodes_iter():
+        if 'r_epik_Ionization_Penalty' in n.struc.property:
+            smile2node[n.canonical_smiles].append(n)
+
+    smile2supernode = defaultdict(list)
+    for key in smile2node:
+        if len(smile2node[key]) > 1:
+            smile2supernode[key].extend(smile2node[key])
+    
+    return smile2supernode
+
+
+def get_ligname(node):
+    return node.short_id_title.split(':')[1].strip()
+
+
+def write_popfile_from_epik(g, delimiter, outname, kT=0.596):
+    """
+    Parse the epik ionization penalty for each ligand in the graph that has muliple protomers/tautomers and 
+    write out the input for the pka_tautomer_correction.py script.
+    """
+    # Find the supernodes in the graph:
+    smile2supernode = extract_supernodes(g)
+    lines = []
+    for key in smile2supernode:
+        penalties = np.array([n.struc.property['r_epik_Ionization_Penalty'] for n in smile2supernode[key]])
+        penalties -=  penalties.min()   # Ionization penalties already reflect normalized weights, but doing this for stability
+        populations = np.exp(-penalties / kT ) / np.sum(np.exp(-penalties / kT ))
+        pop_str = [str(p) for p in populations]
+        lignames = [get_ligname(n) for n in smile2supernode[key]]
+
+        lines.append(delimiter.join(lignames) + delimiter + delimiter.join(pop_str))
+            
+    with open(outname, 'w') as f:
+        f.writelines('\n'.join(lines))
+
+
+def main(argv=None):
+    usage="""
+    Extract the Epik protomer/tautomer ionization state penalties and write out a population file for the pKa tautomer 
+    correction script.
+
+    $SCHRODINGER/run extract_epik_pop_corrs.py map_out.fmp -o epik_populations.txt
+    """
+    parser = argparse.ArgumentParser(usage=usage)
+    parser.add_argument('infile',
+                        type=str,
+                        help="The name of an fmp whose ligands have epik state penalties as molecular properties.")
+    parser.add_argument('-o',
+                        dest='outfile',
+                        type=str,
+                        help="The name of the population file that will be produced, default=epik_populations.txt.",
+                        default='epik_populations.txt')
+    parser.add_argument('-d',
+                        dest='delimiter',
+                        type=str,
+                        help="The delimiter with which to space the text in the population file, default=-",
+                        default='-')
+    args = parser.parse_args(argv)
+
+    g = Graph.deserialize(args.infile)
+    write_popfile_from_epik(g, outname=args.outfile, delimiter=args.delimiter)
+
+
+if __name__ == '__main__':
+    main()
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/hif2a_symbmcorr.py b/fep_benchmark_inputs/fep_plus_inputs/merck/hif2a_symbmcorr.py
new file mode 100644
index 0000000000000000000000000000000000000000..16164f40c8934d21c39ce755c413b4da33d85f87
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/hif2a_symbmcorr.py
@@ -0,0 +1,95 @@
+from schrodinger.application.scisol.packages.fep import graph
+import numpy as np
+import argparse
+from itertools import combinations
+
+import sys
+sys.path.append('../')
+import binding_mode_correction as bmc
+
+
+def get_lignames(edge):
+    sep = edge.short_id_title.split('==>')
+    lig1 = sep[0].split(':')[1].strip()
+    lig2 = sep[1].split(':')[1].strip()
+    return lig1, lig2
+
+
+# Add the symmetry corrections. Specific to the map
+degree_of_symm = {'23':2,
+             '251':2,
+             '256':2,
+             '67':2}
+
+def get_error_before_corrs(g):
+    pred_dgs = []
+    exp_dgs = []
+    for n in g.nodes_iter():
+        ligname = n.short_id_title.split(":")[1].strip()
+        if 'flip' not in ligname:
+            pred_dgs.append(n.pred_dg.val)
+            exp_dgs.append(n.exp_dg.val)
+
+    pred_dgs = np.array(pred_dgs)
+    exp_dgs = np.array(exp_dgs)
+
+    pred_dgs += np.mean(exp_dgs) - np.mean(pred_dgs)
+
+    indices = np.arange(len(exp_dgs))
+    pred_pairwise = np.array([pred_dgs[i] - pred_dgs[j] for i, j in combinations(indices, 2)])
+    exp_pairwise = np.array([exp_dgs[i] - exp_dgs[j] for i, j in combinations(indices, 2)])
+
+    sq_diffs = (exp_pairwise - pred_pairwise)**2
+    boot_rmsds = np.zeros(10000)
+    for b in range(10000):
+        samp_inds = np.random.choice(len(sq_diffs), len(sq_diffs))
+        arr_boot = sq_diffs[samp_inds]
+        boot_rmsds[b] = np.sqrt(arr_boot.mean())
+
+    pair_rmsd = np.sqrt(np.mean((exp_pairwise - pred_pairwise)**2))
+    print('Pairwise RMSD without extra rotamers and symmetry correction = {:.2f} +/- {:.2f} kcal/mol'.format(pair_rmsd, np.std(boot_rmsds)))
+
+
+def main(argv=None):
+    usage="""
+    Apply the symmetry and binding mode correction to a particular map.
+
+    $SCHRODINGER/run symbmcorr.py map_out.fmp -o map_bmcorr_out.fmp
+    """
+    parser = argparse.ArgumentParser(usage=usage)
+    parser.add_argument('infile',
+                        type=str,
+                        help="The name of an out fmp file that contains multiple binding modes.")
+    parser.add_argument('-o',
+                        dest='outfile',
+                        type=str,
+                        help="If entered, the name of the corrected map, default=None.",
+                        default=None)
+    args = parser.parse_args(argv)
+
+    g = graph.Graph.deserialize(args.infile)
+
+    # SYMMETRY CORRECTION
+    kT =0.596
+    for e in g.edges_iter():
+        l1, l2 = get_lignames(e)
+        total_corr = 0
+        # Symmetry correction
+        if l1 in degree_of_symm:
+            total_corr += kT * np.log(degree_of_symm[l1])
+        if l2 in degree_of_symm:
+            total_corr -= kT * np.log(degree_of_symm[l2])
+        e.complex_dg += total_corr
+
+    g.calc_cycle_closure()
+
+    # BINDING MODE CORRECTION
+    mode_nodes, corrections = bmc.correct_multiple_binding_modes(g)
+    bmc.merge_ligand_nodes(g, mode_nodes, corrections)
+    g.calc_cycle_closure()
+
+    if args.outfile is not None:
+        g.write(args.outfile)
+
+if __name__ == '__main__':
+    main()
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/pfkfb3_symbmcorr.py b/fep_benchmark_inputs/fep_plus_inputs/merck/pfkfb3_symbmcorr.py
new file mode 100644
index 0000000000000000000000000000000000000000..ee7dd68150f663b4d8ce620c09928daf6a6b858f
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/pfkfb3_symbmcorr.py
@@ -0,0 +1,65 @@
+from schrodinger.application.scisol.packages.fep import graph
+import numpy as np
+import argparse
+
+
+import sys
+sys.path.append('../')
+import binding_mode_correction as bmc
+
+
+def get_lignames(edge):
+    sep = edge.short_id_title.split('==>')
+    lig1 = sep[0].split(':')[1].strip()
+    lig2 = sep[1].split(':')[1].strip()
+    return lig1, lig2
+
+
+# Add the symmetry corrections. Specific to the map
+degree_of_symm = {'44':2, '46':2, '47':2, '48':2, '49':2} 
+
+
+def main(argv=None):
+    usage="""
+    Apply the symmetry and binding mode correction to a particular map.
+
+    $SCHRODINGER/run symbmcorr.py map_out.fmp -o map_bmcorr_out.fmp
+    """
+    parser = argparse.ArgumentParser(usage=usage)
+    parser.add_argument('infile',
+                        type=str,
+                        help="The name of an out fmp file that contains multiple binding modes.")
+    parser.add_argument('-o',
+                        dest='outfile',
+                        type=str,
+                        help="If entered, the name of the corrected map, default=None.",
+                        default=None)
+    args = parser.parse_args(argv)
+
+    g = graph.Graph.deserialize(args.infile)
+
+    # SYMMETRY CORRECTION
+    kT =0.596
+    for e in g.edges_iter():
+        if e.complex_dg is not None:
+            l1, l2 = get_lignames(e)
+            total_corr = 0
+            # Symmetry correction
+            if l1 in degree_of_symm:
+                total_corr += kT * np.log(degree_of_symm[l1])
+            if l2 in degree_of_symm:
+                total_corr -= kT * np.log(degree_of_symm[l2])
+            e.complex_dg += total_corr
+
+    g.calc_cycle_closure()
+
+    # BINDING MODE CORRECTION
+    mode_nodes, corrections = bmc.correct_multiple_binding_modes(g)
+    bmc.merge_ligand_nodes(g, mode_nodes, corrections)
+    g.calc_cycle_closure()
+
+    if args.outfile is not None:
+        g.write(args.outfile)
+
+if __name__ == '__main__':
+    main()
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/run_all_corrections.sh b/fep_benchmark_inputs/fep_plus_inputs/merck/run_all_corrections.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ae7d3ef5ba095f57b2bde15ea4aaae49f9c5a18a
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/run_all_corrections.sh
@@ -0,0 +1,6 @@
+$SCHRODINGER/run cdk8_symbmcorr.py cdk8_5cei_new_helix_loop_extra/cdk8_5cei_new_helix_loop_extra_out.fmp -o cdk8_5cei_new_helix_loop_extra/cdk8_symbmcorr_out.fmp
+./run_eg5_corrections.sh
+$SCHRODINGER/run hif2a_symbmcorr.py hif2a_automap/hif2a_automap_out.fmp -o hif2a_automap/hif2a_automap_symbmcorr_out.fmp
+#$SCHRODINGER/run pfkfb3_symbmcorr.py pfkfb3_automap/pfkfb3_automap.fmp -o pfkfb3_automap/pfkfb3_automap_symbmcorr_out_fmp
+./run_syk_corrs.sh 
+./run_tnks2_corrs.sh
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/run_eg5_corrections.sh b/fep_benchmark_inputs/fep_plus_inputs/merck/run_eg5_corrections.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9feb75773721f01b7f8758c455b4bca85c9fe523
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/run_eg5_corrections.sh
@@ -0,0 +1 @@
+$SCHRODINGER/run -FROM scisol pka_tautomer_correction.py eg5_extraprotomers/eg5_extraprotomers_out.fmp -o eg5_extraprotomers/eg5_extraprotomers_pkacorr_out.fmp -p eg5_populations_epik.txt -s-
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/run_syk_corrs.sh b/fep_benchmark_inputs/fep_plus_inputs/merck/run_syk_corrs.sh
new file mode 100755
index 0000000000000000000000000000000000000000..0b455dbb45ddff15a7c450b84e9cf12de8f9442e
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/run_syk_corrs.sh
@@ -0,0 +1,2 @@
+$SCHRODINGER/run -FROM scisol binding_mode_correction.py syk_4puz_fullmap/syk_4puz_fullmap_out.fmp -o syk_4puz_fullmap/syk_bmcorr_out.fmp
+$SCHRODINGER/run -FROM scisol pka_tautomer_correction.py syk_4puz_fullmap/syk_bmcorr_out.fmp -p syk_epik_pops.txt -s- -o syk_4puz_fullmap/syk_pkacorr_out.fmp
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/run_tnks2_corrs.sh b/fep_benchmark_inputs/fep_plus_inputs/merck/run_tnks2_corrs.sh
new file mode 100755
index 0000000000000000000000000000000000000000..87a8cdaace0e26b9df986bbe241d141014aa9b07
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/run_tnks2_corrs.sh
@@ -0,0 +1,4 @@
+# 1. Apply the symmetry correction to all ligands except 7.
+$SCHRODINGER/run tnks2_symcorr.py tnks2_fullmap/tnks2_fullmap_out.fmp -o tnks2_fullmap/tnks2_symcorr_out.fmp
+# 2. Apply the pKa correction
+$SCHRODINGER/run -FROM scisol pka_tautomer_correction.py tnks2_fullmap/tnks2_symcorr_out.fmp -pka-file tnks2_macropka.txt -o tnks2_fullmap/tnks2_symcorr_pkacorr_out.fmp -s _
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/setup_and_run.sh b/fep_benchmark_inputs/fep_plus_inputs/merck/setup_and_run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..131180c783e14c871e6364702b8f5e34622a73c3
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/setup_and_run.sh
@@ -0,0 +1,9 @@
+PROTEINS=(cdk8_5cei_new_helix_loop_extra cmet eg5_extraprotomers hif2a_automap pfkfb3_automap shp2 syk_4puz_fullmap tnks2_fullmap)
+for P in ${PROTEINS[*]}
+do
+    mkdir "${P}"
+    cp ${P}.fmp ${P}
+    cd "${P}"
+    "${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME ${P} ${P}.fmp -QARG "-P dev_GPU"
+    cd ../
+done
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/subset_metadata.csv b/fep_benchmark_inputs/fep_plus_inputs/merck/subset_metadata.csv
new file mode 100644
index 0000000000000000000000000000000000000000..0384486f135d01b7a5dfbc24e699cb343320466f
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/subset_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:938f98e529e1ff10516c8b94ea2cd970c4b2aebe981a1d9ba4922e15a1c1d620
+size 819
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/syk_epik_pops.txt b/fep_benchmark_inputs/fep_plus_inputs/merck/syk_epik_pops.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e094fba0057a917104ae724418fd3e4257eaae45
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/syk_epik_pops.txt
@@ -0,0 +1,2 @@
+redocked CHEMBL3265000 ground state-redocked CHEMBL3265000-0.992844680141203-0.0071553198587971075
+CHEMBL3265003 tautomer 1-CHEMBL3265003 tautomer 2-0.5-0.5
\ No newline at end of file
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/tnks2_macropka.txt b/fep_benchmark_inputs/fep_plus_inputs/merck/tnks2_macropka.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5b2fedad0819711fa538df675eddecd1da5d7d3
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/tnks2_macropka.txt
@@ -0,0 +1,9 @@
+pH  7.7
+
+# ligand     ligand      pka
+8c neutral equitorial_8c adjust_10.457
+8d neutral equitorial_8d_10.447
+8f neutral_8f_9.396
+8e adjust neutral_8e_9.39
+8b neutral_8b_7.82
+8a neutral_8a_7.82
diff --git a/fep_benchmark_inputs/fep_plus_inputs/merck/tnks2_symcorr.py b/fep_benchmark_inputs/fep_plus_inputs/merck/tnks2_symcorr.py
new file mode 100644
index 0000000000000000000000000000000000000000..6ccfbe21ca75360833e1db13ec6def732a0ebf93
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/merck/tnks2_symcorr.py
@@ -0,0 +1,65 @@
+from schrodinger.application.scisol.packages.fep import graph
+import numpy as np
+import argparse
+
+
+import sys
+sys.path.append('../')
+import binding_mode_correction as bmc
+
+
+def get_lignames(edge):
+    sep = edge.short_id_title.split('==>')
+    lig1 = sep[0].split(':')[1].strip()
+    lig2 = sep[1].split(':')[1].strip()
+    return lig1, lig2
+
+
+def main(argv=None):
+    usage="""
+    Apply the symmetry and binding mode correction to a particular map.
+
+    $SCHRODINGER/run symbmcorr.py map_out.fmp -o map_bmcorr_out.fmp
+    """
+    parser = argparse.ArgumentParser(usage=usage)
+    parser.add_argument('infile',
+                        type=str,
+                        help="The name of an out fmp file that contains multiple binding modes.")
+    parser.add_argument('-o',
+                        dest='outfile',
+                        type=str,
+                        help="If entered, the name of the corrected map, default=None.",
+                        default=None)
+    args = parser.parse_args(argv)
+
+    g = graph.Graph.deserialize(args.infile)
+
+    # Add the symmetry corrections. Specific to the map
+    degree_of_symm = {}
+    for n in g.nodes_iter():
+        l = n.short_id_title.split(':')[1].strip()
+        if l != '7':
+            degree_of_symm[l] = 2
+        else:
+            print('Ligand 7 does not need the correction.')
+
+
+    # SYMMETRY CORRECTION
+    kT =0.596
+    for e in g.edges_iter():
+        l1, l2 = get_lignames(e)
+        total_corr = 0
+        # Symmetry correction
+        if l1 in degree_of_symm:
+            total_corr += kT * np.log(degree_of_symm[l1])
+        if l2 in degree_of_symm:
+            total_corr -= kT * np.log(degree_of_symm[l2])
+        e.complex_dg += total_corr
+
+    g.calc_cycle_closure()
+
+    if args.outfile is not None:
+        g.write(args.outfile)
+
+if __name__ == '__main__':
+    main()
diff --git a/fep_benchmark_inputs/fep_plus_inputs/misc/galectin3_ffb_oplsdir/custom_2021_4.opls b/fep_benchmark_inputs/fep_plus_inputs/misc/galectin3_ffb_oplsdir/custom_2021_4.opls
new file mode 100644
index 0000000000000000000000000000000000000000..04e83bfb46250450af72e633a55f0de8308137a2
Binary files /dev/null and b/fep_benchmark_inputs/fep_plus_inputs/misc/galectin3_ffb_oplsdir/custom_2021_4.opls differ
diff --git a/fep_benchmark_inputs/fep_plus_inputs/misc/galectin3_ffb_oplsdir/custom_2022_3.opls b/fep_benchmark_inputs/fep_plus_inputs/misc/galectin3_ffb_oplsdir/custom_2022_3.opls
new file mode 100644
index 0000000000000000000000000000000000000000..b1eda545dbd8daf00d0d05c5f4d6a41e9e23950b
Binary files /dev/null and b/fep_benchmark_inputs/fep_plus_inputs/misc/galectin3_ffb_oplsdir/custom_2022_3.opls differ
diff --git a/fep_benchmark_inputs/fep_plus_inputs/misc/run_all_corrections.sh b/fep_benchmark_inputs/fep_plus_inputs/misc/run_all_corrections.sh
new file mode 100755
index 0000000000000000000000000000000000000000..a5da7367340345e85b41bdd23eff0f45c2d9db2c
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/misc/run_all_corrections.sh
@@ -0,0 +1 @@
+$SCHRODINGER/run -FROM scisol binding_mode_correction.py btk_extra_flip/btk_extra_flip_out.fmp -o btk_extra_flip/btk_extra_flip_bmcorr_out.fmp
diff --git a/fep_benchmark_inputs/fep_plus_inputs/misc/setup_and_run.sh b/fep_benchmark_inputs/fep_plus_inputs/misc/setup_and_run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1329bf1edabde72e228252a5a17ff57c6f61e68d
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/misc/setup_and_run.sh
@@ -0,0 +1,16 @@
+PROTEINS=(btk_extra_flip cdk8_koehler hfaah hiv_prot_ekegren)
+for P in ${PROTEINS[*]}
+do
+    mkdir "${P}"
+    cp ${P}.fmp ${P}
+    cd "${P}"
+    "${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME ${P} ${P}.fmp -QARG "-P dev_GPU"
+    cd ../
+done
+
+# Error with forcefield builder in 22-3, so using a custom OPLSDIR:
+mkdir galectin3_extra
+cp -r galectin3_extra.fmp galectin3_ffb_oplsdir galectin3_extra
+cd galectin3_extra
+"${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -OPLSDIR galectin3_ffb_oplsdir -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME galectin3_extra galectin3_extra.fmp -QARG "-P dev_GPU"
+cd ../
diff --git a/fep_benchmark_inputs/fep_plus_inputs/misc/subset_metadata.csv b/fep_benchmark_inputs/fep_plus_inputs/misc/subset_metadata.csv
new file mode 100644
index 0000000000000000000000000000000000000000..c9ec0b5be7a7ebffc0a9b0d7bf4453388e2ac174
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/misc/subset_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:6484802c91d882f8737db1c075ae4c9469a0b24666347ac4aeb5933ec6f78469
+size 532
diff --git a/fep_benchmark_inputs/fep_plus_inputs/opls_stress/setup_and_run.sh b/fep_benchmark_inputs/fep_plus_inputs/opls_stress/setup_and_run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..d5e72b1dee443d44082c4062110beea1cb4d60b7
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/opls_stress/setup_and_run.sh
@@ -0,0 +1,15 @@
+PROTEINS=(chk1_set1 chk1_set2 chk1_set3 chk1_set4 chk1_set5 chk1_set6 chk1_set7 cr_bace1 cr_bace2 fxa_set3 fxa_set4 fxa_set5 fxa_set6 hc_bace1 hc_bace2 pb_bace3)
+for P in ${PROTEINS[*]}
+do
+    mkdir "${P}"
+    cp ${P}.fmp ${P}
+    cd "${P}"
+    "${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME ${P} ${P}.fmp -QARG "-P dev_GPU"
+    cd ../
+done
+
+mkdir fxa_yoshikawa_set
+cp fxa_yoshikawa_set.fmp fxa_yoshikawa_set
+cd fxa_yoshikawa_set
+"${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -vacuum -modify_dihe -ensemble muVT -seed 1 -JOBNAME fxa_yoshikawa_set fxa_yoshikawa_set.fmp -QARG "-P dev_GPU"
+cd ../
diff --git a/fep_benchmark_inputs/fep_plus_inputs/opls_stress/subset_metadata.csv b/fep_benchmark_inputs/fep_plus_inputs/opls_stress/subset_metadata.csv
new file mode 100644
index 0000000000000000000000000000000000000000..99e47fdecbfdd73a26ec031af8e3d13aac30d8e8
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/opls_stress/subset_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f723ee143625bb3cd75f10e5d35feeade14ad7f6c060e91c97fb8c76076d9f06
+size 1578
diff --git a/fep_benchmark_inputs/fep_plus_inputs/post_simulation_corrections.md b/fep_benchmark_inputs/fep_plus_inputs/post_simulation_corrections.md
new file mode 100644
index 0000000000000000000000000000000000000000..1f67e703f1c559823702836cb3e84138235185dd
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/post_simulation_corrections.md
@@ -0,0 +1,69 @@
+## Benchmark subsets with systems that have post simulation corrections
+Here is a breakdown of the corrections applied to the maps. This can be applied automatically wtih `apply_all_corrections.sh`.
+
+Prior to the 22-3 release, pKa/tauotmer and binding mode corrections had to be run seperately from the command line and
+custom scripts. The corrections outlined in this section are for releases 22-2 and earlier and can be streamlined for 
+more recent releases. 
+
+FEP maps and directories that are _not_ listed below require no post processing.
+ 
+###  `charge_annhil/` FEP+ charge-change 
+Every `fmp` file, except `thrombin_whole_map.fmp` requires a pKa correction. The solvent pKas can be found in the accompanying 
+`.txt` files. The are 2 sets of solvent pKas: manually chosen (`*_pka.txt`)or automatically entered with epiK 
+(`*_epikpka.txt`). These pKa files can be used as input to the `pka_tautomer_correction.py` script.
+
+### `fragments/` FEP+ fragements
+There are 2 jak2 maps that require pka/tautomer corrections as well as binding mode corrections. These correction 
+scripts are:
+* `run_jak2_set1_corrs.sh`, which uses `jak2_set1_pka.txt` as input.
+* `run_jak2_set2_corrs.sh`
+ 
+### `gpcrs/` GPCRs
+* A2A: pka, binding mode, and symmetry corrections can be run with `run_a2a_corrs.sh` which uses `a2a_epik_pka.txt` and 
+`a2a_symbmcorr.py`.
+* The output 2 P2Y1 maps can be merged using: 
+    - `$SCHRODINGER/run -FROM scisol merge_graph.py p2y1_meta_sub_out.fmp p2y1_ortho_sub_out.fmp -o p2y1_merged.fmp -sc`
+    
+
+### `jacs_set/` FEP+ R-group set
+* The JNK1 output requires binding mode corrections: 
+    -  `$SCHRODINGER/run -FROM scisol binding_mode_correction.py jnk1_manual_flips_out.fmp -o jnk1_manual_flips_out_bmcorr_out.fmp`
+* The MCL1 map also requires binding mode corrections:
+    - `$SCHRODINGER/run -FROM scisol binding_mode_correction.py mcl1_extra_flips_out.fmp -o mcl1_extra_flips_out_bmcorr_out.fmp`
+    
+    
+### `janssen_bace/` Janssen BACE1 data sets
+* One molecule from the retrospective set from Ciordai et al. requires a pKa correction for one molecule. This can be 
+run using `run_bace_ciordia_retro_corrs.sh`
+* The P2 pocket subset from Keranen et al. requires binding mode corrections. These can be run using 
+`run_bace_keranen_p2_corrs.sh`
+
+### `mcs_docking` MCS docking sets
+* The HNE map has some molecules with multiple protonation states. These can be corrected for using
+    - `$SCHRODINGER/run -FROM scisol pka_tautomer_correction.py hne_500mM_out.fmp -pka-file hne_epik_pka.txt -o hne_500mM_pkacorr_out.fmp`
+
+### `merck/` The public Merck data sets
+* The CDK8 map requires symmetry and binding mode corrections. These can be implemented with `cdk8_symbmcorr.py` script
+like so:
+    -  `$SCHRODINGER/run cdk8_symbmcorr.py cdk8_5cei_new_helix_loop_extra_out.fmp -o cdk8_symbmcorr_out.fmp`
+* The Eg5 map has multiple protomers that can be handled usig `run_eg5_corrections.sh`.
+* Some ligands in the hif2-alpha map have 2 rotamer states whereas other require symmetry corrections. These can be 
+handled with the python script:
+    - `$SCHRODINGER/run hif2a_symbmcorr.py hif2a_automap_out.fmp -o hif2a_automap_symbmcorr.fmp`
+* Most ligands in the PFKFB3 have multiple rotamers whereas some require a symmetry correction, which require the 
+application of the script:
+    - `$SCHRODINGER/run pfkfb3_symbmcorr.py pfkfb3_automap.fmp -o pfkfb3_automap_symbmcorr_out_fmp`
+* Some ligands in the SYK map have different protomers, tautomers, and rotamers, which can be addressed using `run_syk_corrs.sh`.
+* The TNKS2 requires correcting for multiple protomers and one symmetric rotamer state. These can be corrected using
+` run_tnks2_corrs.sh`.
+
+### `misc/` Miscellaneous
+* Some of the ligands in the BTK map have 2 rotamer states that have been added to the map. These can be accounted for
+with 
+    - `$SCHRODINGER/run binding_mode_correction.py btk_extra_flip_out.fmp -o btk_extra_flip_bmcorr_out.fmp`
+
+### `waterset/` FEP+ buried water set
+* The scytalone dehydratase map has a bespoke pKa correction script that was written for the validation of the FEP+'s
+GCMC method. The corrections can be applied using
+    - `$SCHRODINGER/run sd_analysis_tools.py -i scyt_dehyd_out.fmp -o scyt_dehyd_pkacorr_out.fmp -d macro`
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/scaffold_hopping/setup_and_run.sh b/fep_benchmark_inputs/fep_plus_inputs/scaffold_hopping/setup_and_run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9e6d9ee418cfdd13fccea98b361668d15eae84f3
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/scaffold_hopping/setup_and_run.sh
@@ -0,0 +1,10 @@
+PROTEINS=(Bace1_4zsp CHK1_3u9n_corehop Era_2q70 Fxa_2ei8 TPSB2_3v7t)
+for P in ${PROTEINS[*]}
+do
+    mkdir "${P}"
+    cp ${P}.fmp ${P}
+    cd "${P}"
+    "${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:50 -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME ${P} ${P}.fmp -QARG "-P dev_GPU"
+    cd ../
+done
+
diff --git a/fep_benchmark_inputs/fep_plus_inputs/scaffold_hopping/subset_metadata.csv b/fep_benchmark_inputs/fep_plus_inputs/scaffold_hopping/subset_metadata.csv
new file mode 100644
index 0000000000000000000000000000000000000000..c5e31fdbbb663a572bb54e01657ff703af8950f5
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/scaffold_hopping/subset_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:12df3ce9790a92edeed3a1bf1b2af4a98e16f92859588ed4fc6d8edf636f3cee
+size 734
diff --git a/fep_benchmark_inputs/fep_plus_inputs/waterset/run_all_corrections.sh b/fep_benchmark_inputs/fep_plus_inputs/waterset/run_all_corrections.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5017de04b6f166ce5eb279f4ead759b75914f042
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/waterset/run_all_corrections.sh
@@ -0,0 +1,2 @@
+$SCHRODINGER/run sd_analysis_tools.py -i scyt_dehyd/scyt_dehyd_out.fmp -o scyt_dehyd/scyt_dehyd_pkacorr_out.fmp -d macro
+$SCHRODINGER/run -FROM scisol binding_mode_correction.py throm_nozob_hip75/throm_nozob_hip75_out.fmp -o throm_nozob_hip75/throm_nozob_hip75_bmcorr_out.fmp
diff --git a/fep_benchmark_inputs/fep_plus_inputs/waterset/sd_analysis_tools.py b/fep_benchmark_inputs/fep_plus_inputs/waterset/sd_analysis_tools.py
new file mode 100644
index 0000000000000000000000000000000000000000..0ac8bfe43008f0252af6c78555985c4cef66e0d1
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/waterset/sd_analysis_tools.py
@@ -0,0 +1,146 @@
+import numpy as np
+from copy import deepcopy
+from schrodinger.application.scisol.packages.fep import graph
+from schrodinger.application.scisol.packages.fep import fep_stats
+from schrodinger.application.desmond.measurement import Measurement
+from itertools import combinations
+
+
+from scipy.optimize import minimize
+
+
+def selection_penaly(pka, ph=7., protonated=True):
+    """
+    The free energy to select out the either the protonated or deprotonated state of a molecule in solvent.
+
+    Note
+    ----
+    The way to think about it is via the grand canonical ensemble. These penalties are the ratios of two grand canonical
+    partition functions where one state has been removed.
+
+    Parameters
+    ----------
+    ph = float
+        The pH of the solvent.
+    pka: float
+        The pKa of the protonated form.
+    protonated: bool
+        Whether to spit out the penalty to select either the protonated form, or deprotonated form.
+    """
+    top = 10 ** (pka - ph)
+    if protonated:
+        return -0.596 * np.log(top / (1 + top))
+    else:
+        return -0.596 * np.log(1 / (1 + top))
+
+
+def solvent_penalty(pka1, pka2, ph=7):
+    """
+    Apply the relative free energy penalty to isoloate the neutral forms of two ligands. Used to for the
+    pKa correction of the SD map.
+    """
+    top1 = 10 ** (pka1 - ph)
+    top2 = 10 ** (pka2 - ph)
+    return -0.596 * np.log((1 + top1) / (1 + top2))
+
+
+def apply_solvent_penalty(g_pka, pka_dict):
+    """
+    Calculate the solvent pKa penalty for the ligands in an fmp map.
+
+    Parameters
+    ----------
+    g_pka: fmp map
+        The map whose entries will be changed in place to reflect the pka correction.
+    pka_dict: dict
+        The dictionary that stores (by ligand name) the macro pKas of the ligands.
+    """
+    for e in g_pka.edges_iter():
+        l1 = e.short_id_title.split('==>')[0].split(':')[1].strip()
+        l2 = e.short_id_title.split('==>')[1].split(':')[1].strip()
+        corr = solvent_penalty(pka_dict[l1], pka_dict[l2])
+        unc = e.complex_dg.unc
+        val = e.complex_dg.val
+        e.complex_dg = Measurement(val + corr, unc)
+    g_pka.calc_cycle_closure()
+
+def pretty_print_fmp(g):
+    """
+    Print the statistics from an fmp file
+    """
+    results = fep_stats.calculate(g)
+    for item in results:
+        print(item, results[item])
+
+import argparse
+def get_arg_parser():
+    # Setup a parser of the command-line arguments
+    parser = argparse.ArgumentParser(description="Program to automatically apply the pKa correction to the scytalone"
+                                                 "dehydratase map.")
+    parser.add_argument('-i', '--infile', type=str,
+                        help="the name of the scytalone out fmp file that.")
+    parser.add_argument('-o', '--outfile', type=str,
+                        help="the name of the output fmp that has the pKa correction appied.")
+    parser.add_argument('-d', '--dict', type=str, choices=['macro', 'fitted'],
+                        help="the type of pKa dictionary to use: 'macro' for the pKas predicted by macropka and 'fitted'"
+                             " for the pKas that have been optimized to reduce pairwise RMSE, default=macro", default='macro')
+    parser.add_argument('--optimize', action='store_true',
+                        help='Whether to minimize the pairwise RMSE by altering the pKas of 2d, 3d, 6d, and 8d.', default=False)
+    return parser
+
+
+if __name__ == '__main__':
+    args = get_arg_parser().parse_args()
+
+    # The prediction from macropKa on simplified versions of the ligands.
+    #PKA_DICT = {'2d': 6.33, '3d': 9.26, '4d': 5.45, '5d': 4.06, '6d': 7.09, '7d': 5.42, '8d': 7.13}
+    # 14th January 2019
+    # -----------------
+    # MacropKa predicts a value of 9.26 for compound 3d. However, there is good experimental evidence that the pKa of
+    # 3d is 8.0. So using that value for ligand 3d.
+    #PKA_DICT = {'2d': 6.33, '3d': 8.0, '4d': 5.45, '5d': 4.06, '6d': 7.09, '7d': 5.42, '8d': 7.13}
+    PKA_DICT = {'2d': 5.60, '3d': 8.89, '4d': 5.23, '5d': 4.06, '6d': 7.09, '7d': 3.61, '8d': 7.10}
+    # The result from optimizing the pKas of 2d, 3d, 6d and 8d to minimize the pairwise RMSE of the map.
+    OPT_PKA_DICT = {'2d': 6.11923504, '3d': 8.26555333, '4d': 5.45, '5d': 4.06, '6d': 8.0862216, '7d': 5.42, '8d': 7.62419523}
+
+    # Read in the graph:
+    g = graph.Graph.deserialize(args.infile)
+
+    if args.dict == 'macro':
+        pka_dict = PKA_DICT
+    elif args.dict == 'fitted':
+        pka_dict = OPT_PKA_DICT
+    else:
+        raise Exception('Unable to recognize the option for --dict. Please choose a valid option.')
+
+    if args.optimize:
+        # Minimize the pKas from the starting dict subject to the constraint that they can be no more than 1 log unit away from their starting value.
+        X0 = np.array((pka_dict['2d'], pka_dict['6d'], pka_dict['8d']))
+        def pairwise_error_constraint(pkas):
+            """
+            Defining the function that will be minimized.
+            """
+            if np.any(np.abs(X0 - pkas) > 1):
+                return np.inf
+            else:
+                g_pka_corr = deepcopy(g)
+                pka_dict_mod = {'2d': pkas[0], '3d': 8.0, '4d': 5.45, '5d': 4.06, '6d': pkas[1], '7d': 5.42, '8d': pkas[2]}
+                apply_solvent_penalty(g_pka_corr, pka_dict_mod)
+                r = fep_stats.calculate(g_pka_corr)
+                return r['RMSE Edgewise'].val
+
+        print('\nOptimizing pKas of 2d, 6d and 8d to minimize the edgewise RMSE...')
+        result = minimize(fun=pairwise_error_constraint, x0=X0, method='Nelder-Mead', options={'maxiter': 100})
+        pka_dict['2d'] = result.x[0]
+        pka_dict['6d'] = result.x[1]
+        pka_dict['8d'] = result.x[2]
+        print('... Optimization compled.')
+        print('Fitted values are:')
+        print(pka_dict)
+
+    # Apply the pKa correction:
+    g_pka_corr = deepcopy(g)
+    apply_solvent_penalty(g_pka_corr, pka_dict)
+    #print('\nNew results:')
+    #pretty_print_fmp(g_pka_corr)
+    g_pka_corr.write(args.outfile)
diff --git a/fep_benchmark_inputs/fep_plus_inputs/waterset/setup_and_run.sh b/fep_benchmark_inputs/fep_plus_inputs/waterset/setup_and_run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..01b61afb6eda2844522d2bacb1a2be783d2b822e
--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/waterset/setup_and_run.sh
@@ -0,0 +1,9 @@
+PROTEINS=(hsp90_kung brd41_ASH106 taf12 scyt_dehyd chk1 throm_nozob_hip75 urokinase hsp90_woodhead)
+for P in ${PROTEINS[*]}
+do
+    mkdir "${P}"
+    cp ${P}.fmp ${P}
+    cd "${P}"
+    "${SCHRODINGER}/fep_plus" -HOST bolt_cpu -SUBHOST bolt_gpu -ppj 2 -ffbuilder -ff-host bolt_cpu:30 -time 20000.0 -vacuum -ensemble muVT -seed 1 -JOBNAME ${P} ${P}.fmp -QARG "-P dev_GPU"
+    cd ../
+done
diff --git a/fep_benchmark_inputs/fep_plus_inputs/waterset/subset_metadata.csv b/fep_benchmark_inputs/fep_plus_inputs/waterset/subset_metadata.csv
new file mode 100644
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--- /dev/null
+++ b/fep_benchmark_inputs/fep_plus_inputs/waterset/subset_metadata.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a3416e1dec300d7aabd7c3581530be27548b1029a9c76ff0430714241199e84b
+size 839
diff --git a/fep_benchmark_inputs/structure_inputs/README.md b/fep_benchmark_inputs/structure_inputs/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..cac09bcf8d4d14687835ec7aefcc600ff0d3da0f
--- /dev/null
+++ b/fep_benchmark_inputs/structure_inputs/README.md
@@ -0,0 +1,30 @@
+# Benchmark structural inputs
+The protein and ligand structures of the benchmark. In total, there are 103 protein structures 
+associated ligand binding poses that have been seperated in 14 sub-directories that indicate the were the input data was
+adapted from. 
+
+## Subset directories
+The names of each directory and the corresponding subset title in the [accompanying manuscript](https://doi.org/10.26434/chemrxiv-2022-p2vpg).
+
+* `bayer_macrocycles/`: Bayer Macrocycles
+* `charge_annhil/`: FEP+ charge change set
+* `fragments/`: FEP+ fragment data set
+* `gpcrs/`: GPCRs
+* `jacs_set/`: FEP+ R-group set
+* `janssen_bace/`: Janssen BACE1 data sets
+* `macrocycles/`: FEP+ macrocycles
+* `mcs_docking/`: MCS docking sets
+* `merck/`: The public Merck data set
+* `misc/`: Miscellaneous data sets
+* `opls_stress/`: OPLS stress set
+* `scaffold_hoping/`: FEP+ scaffold hopping
+* `waterset/`: FEP+ buried water set
+
+### Subset directory contents
+Each directory contains 
+* `subset_metadata.csv`. Metadata on each subsystem, the file naming scheme and the PDB each model was based on.  
+* `*_ligands.sdf` The ligands along with additional rotomers and protomer/tautomer states. Each ligand is tagged with the
+experimental binding free energy (in kcal/mol). 
+* `*_protien.pdb` The target structure.
+* `*_edges.csv` The edges of the perturbation graph along with experimental relative binding free energy.
+
diff --git a/fep_benchmark_inputs/structure_inputs/bayer_macrocycles/ftase_extraligs_custcore_stereo_edges.csv b/fep_benchmark_inputs/structure_inputs/bayer_macrocycles/ftase_extraligs_custcore_stereo_edges.csv
new file mode 100644
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--- /dev/null
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