Background: The user has a cluster model PDB file that has already been cleaned/trimmed/protonated. A Psi4 FSAPT computation has been run on this PDB structure wherein the species of interest (e.g. the chorismate of chorismate mutase) is listed as the first interacting body and the enzyme is the second interacting body. The atom ordering of the first body is in the same order as in the PDB file, and the atom ordering of the second body is in the same order as in the PDB file, but the overall atom indices do not need to be the same (e.g. it is okay that the chorismate is listed as the first body in the FSAPT calculation, but it does not appear first in the PDB file, as long as the order of the chorismate atoms is the same and the order of the rest of the enzyme atoms is the same). NOTE: If there is more than one seed fragment, the fragments must be in the same order in the first body as they are in the pdb, even if they are noncontiguous fragments. The user wishes to automate the process of identifying the unique side/main chains and waters present in the cluster model and computing the FSAPT interaction between the first body and each of these functional groups. Example using GNMT with the SAM and GLY (A:293,A:294) as the seed

1. Identify functional group atoms

• The gen-FG-analysis.py script is a rudimentary script that can be used to identify which atoms of the cluster model PDB correspond to residue main chains, residue side chains, and waters. Because the atom indices between the PDB and the FSAPT computation may be different (e.g. with chorismate it is located in the middle of the PDB ordering but as the first body in the FSAPT calculation) the atom indices printed in the outputfile will be shifted according to the expected atom indices in the FSAPT calculation. Example script usage:

  input : python3 ~/git/RINRUS/bin/FSAPT/gen-FG-atomIDs.py -p template_27_1.pdb -s A:293,A:294 output: pdbFG.dat

• The output pdbFG.dat file contains info on: how many atoms are in the structure (line 1), the atom names of the first body (line 2), and the names and corresponding shifted atom indices for the functional groups identified by the script (for example, the side chain of residue 7 of chain A would correspond to atoms 25-46 in the geom.xyz script generated by the FSAPT calculation in the fsapt directory for this computation).

2. Calculate all of the functional group atom interactions with the first body

• Now that the atom indices of the functional groups have been identified and summarized in the generated pdbFG.dat file, we can automate the calculation of their interaction energies with the first body using the analyze-FG-SAPT.py script. The script needs to be run within the fsapt directory output by the FSAPT computation in the computation's scratch directory as this directory contains the data files required for calculating the energies among the user-specified functional groups/partitions. Assuming that the pdbFG.dat file is located in the directory before the fsapt directory (this location can be changed with the flag -p ) the script can be run as-is. o What the script does is uses the information within pdbFG.dat to generate file fA.dat, which contains the functional group information for the first body (by default using the whole first body [i.e. the whole chorismate], though this can be changed to indicate only a particular functional group of the first body [i.e. only one of the carboxylates] using the -a flag), and then file fB.dat, which contains the functional group information for the second body. The script will begin by setting fB.dat to the first functional group (specifically the enzyA within fB.dat will correspond to the atom indices of the first functional group and enzyB will correspond to the atom indices of the rest of the enzyme of the second body). The Psi4 fsapt.py script will then be automatically executed to calculate the FSAPT interaction energies, and then the specific interactions between the two bodies of interest (specifically enzyA of fB.dat and seedA of fA.dat) will be saved. The fB.dat file is then re-written using the next functional group in the pdbFG.dat file as the next enzyA functional group, and the process is repeated until all of the functional groups interaction energies has been computed. Example usage (within the fsapt directory):

  input: python3 ~/git/RINRUS/bin/FSAPT/analyze-FG-SAPT.py -path /home/ndyonker/git/psi4/objdir/stage/share/psi4/fsapt/ output: ../FG-SAPT.dat

3. (Additional) Gather probe counts and arpeggio interactions for functional group atoms The gen-FG-analysis-probe.py script counts the contacts for the functional groups interacting with a user-specified seed. Requires a probe file to have been run on the PDB. Example usage: o python3 gen-FG-analysis-probe.py -p 2cht.10000.probe -s A:128 output: FG-probe.dat which lists the functional groups and the number of contacts with the seed

The gen-FG-analysis-arpeggio.py script counts the interactions for the functional groups interacting with a user-specified seed. Requires an arpeggio contacts file to have been run on the cluster PDB. Example usage: o python3 gen-FG-analysis-arpeggio.py -c res_17_h.contacts -p res_17_h.pdb -s A/128 output: FG-arpeggio.dat which lists the functional groups and the number of given interaction types. The order of the interaction types column is the same as in the contacts file, which can be found in the README of Arpeggio

The sapt2rins.py script generates the res_atoms.dat, which then allows you to create models for quantum chemistry software packages (step 9 of the original workflow)

Example usage: o python3 sapt2rins.py -p ../FG-SAPT.dat -c ../contact_counts.dat -s A:293,A:294

input: python3 ~/git/RINRUS_master/bin/FSAPT/sapt2rins.py -p FG-SAPT.dat -c contact_counts.dat -s A:293,A:294 will generate res_atoms.dat
output: res_atoms.dat