Paper Info
Title
A Python tool to set up relative free energy calculations in GROMACS
Abstract
Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of finding a common substructure and mapping the transformation to be applied. Here we present a tool, -, that automatically generates all the input files needed to perform relative solvation and binding free energy calculations with the MD package GROMACS. When combined with Lead Optimization Mapper (LOMAP; Liu et al. in J Comput Aided Mol Des 27(9):755–770, ), recently developed in our group, - allows fully automated setup of relative free energy calculations in GROMACS. Taking a graph of the planned calculations and a mapping, both computed by LOMAP, our tool generates the topology and coordinate files needed to perform relative free energy calculations for a given set of molecules, and provides a set of simulation input parameters. The tool was validated by performing relative hydration free energy calculations for a handful of molecules from the SAMPL4 challenge (Mobley et al. in J Comput Aided Mol Des 28(4):135–150, ). Good agreement with previously published results and the straightforward way in which free energy calculations can be conducted make - a promising tool for automated setup of relative solvation and binding free energy calculations.
Year
DOI
Venue
2015
10.1007/s10822-015-9873-0
Journal of Computer-Aided Molecular Design
Keywords
DocType
Volume
Hydration free energy,Transfer free energy,Free energy calculation,Automated setup
Journal
29
Issue
ISSN
Citations 
11
0920-654X
3
PageRank 
References 
Authors
0.43
4
2
Name
Order
Citations
PageRank
Pavel V. Klimovich1383.36
David L. Mobley221920.01