[gmx-users] g_mmpbsa: MM-PBSA method for GROMACS
rashkush at gmail.com
Fri Jun 13 16:32:16 CEST 2014
Dear Prof. David van der Spoel,
Thank you very much for considering g_mmpbsa for the GROMACS repository. We
have a discussion on the same and will try to patch g_mmpbsa in the
repository. Presently, we do not know how to integrate compilation
procedure of g_mmpbsa with the GROMACS package as APBS libraries are
required during compilation and Fortran compiler are required for the
Since I am travelling these days, hope we could able to work on the same in
a month and so.
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi, India.
On Tue, Jun 10, 2014 at 1:42 AM, David van der Spoel <spoel at xray.bmc.uu.se>
> On 2014-06-09 21:17, Rashmi wrote:
>> Dear GROMACS users,
>> We have developed a new tool,
>> *g_mmpbsa* for GROMACS to carry out the MM-PBSA calculations. It uses
>> APBS libraries for the Poisson-Boltzmann calculations.
>> Include SASA, SAV and WCA
>> non-polar models
>> - It inherits threading (OpenMP) functions from APBS
>> - Simultaneously calculate
>> energy contribution
>> of residue
>> to binding
>> Details of this
>> are given in the following link:
>> Its implementation and testing are discussed in the following publication:
>> We would appreciate for suggestions
>> improvment of
>> this tool.
>> With Regards,
>> School of Computational and Integrative Sciences,
>> Jawaharlal Nehru University,
>> New Delhi
>> 110067, India.
>> Why not upload a patch to http://gerrit.gromacs.org ?
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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