[gmx-users] MM-GB/SA analysis in Gromacs

andrea spitaleri spitaleri.andrea at hsr.it
Thu Nov 29 13:32:56 CET 2012

Dear all,

I would like to bring to your attention this paper 
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046902 in which we made a tool 
to perform MM/PBSA binding free energy calculation in automatic fashion, using torque/pbs parallel 
system implemented in most clusters. The input of the tools are just the xtc trajectory, the tpr and 
eventually the index file. It does perform the computational alanine scanning (CAS) too. The tool is 
available upon request. Further details on the paper.



On 11/29/2012 10:42 AM, Anna Marabotti wrote:
> Dear gmx-users,
> I ran several MD simulations using Gromacs 4.5.4 version, and now I'd
> need to calculate binding free energies using the MM-GBSA method. I
> searched through the manual and through the gmx-users archive, but I
> didn't find a way to do it. I found an old post in which it appeared
> that in the version 4.5 this possibility would have been available
> (http://lists.gromacs.org/pipermail/gmx-users/2010-July/052302.html),
> but it seems to me that this kind of analysis has not been implemented yet.
> In another more recent post, I see that somebody has used mdrun -rerun
> in order to perform calculations, but I don't understand the correct
> procedure to use (apart from the suggestion of using .trr instead of
> .xtc files in order to avoid errors).
> Does anyone have suggestions in order to do this analysis with Gromacs
> trajectories, before I make these calculations with another program?
> Many thanks in advance and best regards
> Anna

Andrea Spitaleri PhD
Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele
Centro di Genomica Traslazione e Bioinformatica
Biomolecular NMR Laboratory Dibit2 Basilica 3A2
Via Olgettina 58
20132 Milano
Tel: 0039-0226434348
Fax: 0039-0226434153

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