GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning

Published: 1 January 2015| Version 1 | DOI: 10.17632/7xrctf55xx.1
C. Paissoni, D. Spiliotopoulos, G. Musco, A. Spitaleri


This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract GMXPBSA 2.1 is a user-friendly suite of Bash/Perl scripts for streamlining MM/PBSA calculations on structural ensembles derived from GROMACS trajectories, to automatically calculate binding free energies for protein–protein or ligand–protein complexes [R.T. Bradshaw et al., Protein Eng. Des. Sel. 24 (2011) 197–207]. GMXPBSA 2.1 is flexible and can easily be customized to specific needs and it is an improvement of the previous GMXPBSA 2.0 [C. Paissoni et al., Comput. Phys. Commun. (2014), 185,... Title of program: GMXPBSA 2.1 Catalogue Id: AETQ_v1_1 Nature of problem Calculates the Molecular Mechanics (MM) data (Lennard-Jones and Coulomb terms) and the solvation energy terms (polar and nonpolar terms respectively) from an ensemble of structures derived from GROMACS molecular dynamics simulation trajectory. These calculations are performed for each single component of the simulated complex, including protein and ligand. In order to cancel out artefacts an identical grid setup for each component, including complex, protein and ligand, is required. Performs sta ... Versions of this program held in the CPC repository in Mendeley Data AETQ_v1_0; GMXPBSA 2.0; 10.1016/j.cpc.2014.06.019 AETQ_v1_1; GMXPBSA 2.1; 10.1016/j.cpc.2014.09.010



Molecular Biology, Biological Sciences, Computational Physics