[gmx-users] MMPBSA with GROMACS: a new revised tool

andrea andrea.spitaleri at iit.it
Mon May 26 03:45:04 CEST 2014

Dear all,

We are very pleased to announce the release of GMXPBSA 2.0 tool to 
calculate binding free energy under the MM/PBSA approximation. This 
version is a complete rewrite of our previous GMXAPBS tool. This tool 
exploits the native GROMACS 4.5 and later version trajectories. Beyond 
GROMACS, you need to install only APBS program to solve the PB 
equations. The installation procedure is very easy, just untar the 
source code and that's it!
This new version now reads an INPUT file where the user can set all the 
needed setting.
Our tool can:

1. calculate MM/PBSA on a single trajectory
2. can perform CAS (Computational Alanine scanning) calculations a 
3. simultaneously calculate MM/PBSA on a set of trajectories (i.e. to 
compare different ligands)
4. can perform interface interaction on protein-protein or 
protein-peptide (simultaneously CAS on the binding interface)
5. statistical analysis on the results

The tool can be used upon request. Feel free to contact me.



Andrea Spitaleri PhD
D3 - Drug Discovery & Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
ORCID: http://orcid.org/0000-0003-3012-3557

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