Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] aetq_v1_1.tar.gz(5255 Kbytes)|
|Manuscript Title: GMXPBSA 2.1: a GROMACS tool to perform MM/PBSA and computational alanine scanning|
|Authors: C. Paissoni, D. Spiliotopoulos, G. Musco, A. Spitaleri|
|Program title: GMXPBSA 2.1|
|Catalogue identifier: AETQ_v1_1|
Distribution format: tar.gz
|Journal reference: Comput. Phys. Commun. 186(2015)105|
|Programming language: Bash, Perl.|
|Computer: Any computer.|
|Operating system: Linux, Unix OS.|
|RAM: 2147483648 bytes|
|Supplementary material: A table of added keywords is available.|
|Keywords: Molecular dynamics simulation, Binding Free Energy, Virtual screening, GROMACS, Computational Alanine Scanning, MM/PBSA.|
External routines: Any APBS version (http://www.poissonboltzmann.org/apbs/) and GROMACS version 4.5 or later installations (http://www.gromacs.org). Optionally LaTeX.
Does the new version supersede the previous version?: Yes
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 statistical analysis on the extracted data and comparison with wild-type complex in the case of either computational alanine scanning or calculations on a set of simulations. Evaluates possible outliers in the frames extracted from the simulations during the binding free energy calculations.
The tool combines the freely available programs GROMACS and APBS to:
Reasons for new version:
We had a lot of feedback from our previous GMXPBSA 2.0 publication suggesting improvements. There were also some bugs that required to be fixed urgently in order to keep the program working properly.
Summary of revisions:
In the update version of GMXPBSA 2.1 we include the following changes:
Input format files compatible with GROMACS engine 4.5 and later versions. Availability of the force field or of the topology files.
On a single core Lennard-Jones, Coulomb and nonpolar solvation terms calculations a require few minutes. The time required for polar solvation terms calculations depends on the system size.
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