This provided a fairly basic tool for setting up relative free energy calculations for GROMACS; however, we have been working with the authors of FESetup, a much more general and better-developed tool which produces inputs for a variety of simulation packages, on testing relative free energy calculations with their workflow. In our view, FESetup should be seen as replacing/superseding alchemical-setup, therefore we are no longer maintaining this tool and it is retained here for legacy reasons.
Script: alchemical_setup.py
An automatic setup of relative free energy calculations.
The tool generates input files needed to perform relative solvation and binding free energy calculations with GROMACS.
To provide more details on the algorithmic side, we achieve the above by performing the following steps:
.top
and .gro
file names, one of its attributes will be reserved for a dictionary to store the atom indices mapping)[bonds]
, [angles]
, and [dihedrals]
directives,map.txt
file[atoms]
directive read in and store appropriately all the fields of the [atoms]
directive for both .top
files to avoid duplicates, skip the MCSS atoms of molecule B assign new atom names sort atoms by their new name[atomtypes]
directive[pairs]
directive.gro
file
.gro
file.gro
file.top
fileHelp for alchemical_setup.py
(obtained with python alchemical_setup.py -h
) is:
-h, --help show this help message and exit
-m MAPTXT The atom map .txt file.
-a TOP_A The .top file of molecule A.
-b TOP_B The .top file of molecule B.
-s MCSS The substructure .mol2 file.
-o OUT_DIR The output directory name.
-v VERBOSE Verbosity.