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

Ankita naithani ankitanaithani at gmail.com
Fri Feb 1 12:59:14 CET 2013

Hi Andrea,

Thank you so much for bringing forth the paper. I have performed a MD
simulation and would very much like to use the tool mentioned in the
paper to calculate the binding free energy.
Is it possible for you to kindly give me an access to the same and
also a brief explanation as to how to use the same?

My email id is ankitanaithani1 at gmail.com

Best Wishes


On Thu, Nov 29, 2012 at 12:32 PM, andrea spitaleri
<spitaleri.andrea at hsr.it> wrote:
> 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.
> Regards,
> and
> 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
> Italy
> Tel: 0039-0226434348
> Fax: 0039-0226434153
> http://sites.google.com/site/andreaspitaleri/
> http://www.linkedin.com/in/andreaspitaleri
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Ankita Naithani

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