Re: [AMBER] regarding mm-pbsa calculation

From: Ray Luo <rluo.uci.edu>
Date: Fri, 4 Mar 2016 21:32:14 -0800

Hi Neha,

How about you turn off the entropy calculation first, i.e. the nmode
calculation? It's very slow and uses huge amount of memory. Maybe it's
reaching the limit of your computing power ...

All the best,
Ray

--
Ray Luo, Ph.D.
Professor
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Fri, Mar 4, 2016 at 8:58 PM, neha chaudhary
<nehachaudhary769.gmail.com> wrote:
> Hello Sir,
>
> I want to run MMPBSA calculations for my protein-ligand complex. I have
> extracted snapshots and when I running binding_energy.mmpbsa script as
> given in the documentation page
> *http://ambermd.org/tutorials/advanced/tutorial3/section3.htm
> <http://ambermd.org/tutorials/advanced/tutorial3/section3.htm>*, it seems
> run is going on but it is stuck at :
>
> Calculating energy / entropy contributions
>     Calc contrib for ./snapshot_com.crd.1
>         Checking atom numbers
>         Calc MM/GB/SAS
>         Generate PDB
>         Center PDB
>         Minimize structure and calc entropy
>
> I am attaching binding_energy.log herewith. Please help.
>
> Best Regards,
>
> *Neha*
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himachal Pradesh,
>
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Received on Fri Mar 04 2016 - 22:00:02 PST