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
-------------------------------------------------------------
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
