[gmx-users] MMPBSA with GROMACS: a new revised tool
zhiyue at umaryland.edu
Mon May 26 04:31:46 CEST 2014
Thanks for your message! I noticed the manuscript published on J. Chem.
Inf. Model. was released online today (
On Sun, May 25, 2014 at 5:55 PM, andrea <andrea.spitaleri at iit.it> wrote:
> 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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Graduate Research Assistant
Computer-Aided Drug Design Center
School of Pharmacy
University of Maryland
20 Penn St, Rm S612
Baltimore, MD 21201
Email:zhiyue at umaryland.edu, zhiyue at umd.edu
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