FEP+ Utilities

The following utilities and scripts are available for use in conjunction with FEP+. Click the utility or script name to see its command-line help message.

extract_fmpdb.py

Script to extract the content of a .fmpdb archive.

fep_groups.py

Script to accurately predict affinities for ligands with multiple low energy ionization or tautomeric states. The script reads a map file (.fmp) with the ligands in the various tautomeric and ionization states, and a population file that specifies the population of each tautomeric or ionization state. The input map file should come from an FEP+ job run on the tautomers and protonation states of the ligands of interest. The population file lists the ligands, one ligand per line. For each ligand, the line contains a list of the titles for the ligand states, then a list of populations for these states. The populations can be constructed, for example, from chemical knowledge, from Epik state penalties, or from Jaguar pKa values. If populations defined in a supplied population file does not match with the groups determined for the input .fmp file by the script, an error message fully lists the conflicting groups.

fep_pose_builder.py

Script for generating poses for FEP+ calculations, integrating reference ligand selection, ligand alignment, and clash resolution.

fmp2excel.py

Script to write out a CSV file or Excel spreadsheet from a .fmp file. The file is not exactly the same as that produced from the FEP+ Panel — Map Tab, but it contains the same data. The canonical SMILES string is included in the output for files from a small molecule, covalent ligand, or protein FEP job. You can optionally perform cycle closure analysis with the -cycle-closure option.

fmp2pdf.py

Script to write out a PDF file from a .fmp file.

fmp_info.py

Script to process a .fmp file and provide a comprehensive overview of various graph properties.

merge_fmpdb.py

Script to merge a list of .fmpdb files into a single file. If the files have the same contents, the latters in the list will overwrite the formers.

merge_graph.py

Script to merge two separate graphs into one and write out as one .fmp file.

protein_fep_ph_dependence.py

Script to apply pKa-based corrections to protein FEP binding results at one or two pH values and calculate the pH dependence of binding free energy. This analysis can also be run as part of the fep_plus workflow by specifying the -ph option.

reanalyze_fep.py

Script to reanalyze FEP+ simulations with a given begin-time and end-time in ps.

same_graph.py

Script to generate a new .fmp file from an existing .mae or .fmp file, but only choose edges that is in the existing .fmp file. Graph optimization parameters are taken from template.fmp if they are not specified.

split_graph.py

Scrip to split a .fmp file into several smaller graphs, each with no more than <num> edges (default: 10), and write them out as <output>_1.fmp, <output>_2.fmp and so on.