Re: [AMBER] Error with MM-PBSA perl file for pairwise residue decomposition

From: Bill Miller III <brmilleriii.gmail.com>
Date: Fri, 25 Mar 2011 07:07:45 -0400

Have you tried running the calculation on only a few frames, just to make
sure it will work? I would say if it works on only a few frames, then it
would appear to be a memory issue, but if it will not work for only a few
frames, then the issue is something else entirely. Just a suggestion.

-Bill

On Fri, Mar 25, 2011 at 6:18 AM, Monika Sharma <mondyn.gmail.com> wrote:

> Hello,
>
> Thanks for the reply. But I have not killed the job. First time I waited
> for
> more than a day. But the file was stuck at that reading point. I wrote so,
> because I could not see any such parsing program or any such program which
> I
> could related to PBSA calculation while I checked the list of running
> programs using 'ps -A' or 'top' linux command. Also I used the output
> files
> from the run and tried to run the mm_pbsa_stastistics.pl alone on the
> *out*
> files as
>
> nohup ~/SWare/amber10/src/mm_pbsa/mm_pbsa_statistics.pl 2 2
> snap_statistics.in snap_statistics.out &
>
> As I could monitor the command running as mm_pbsa_statistics.pl using
> 'top', it seemed the command ran for about an hour, and then it just
> disappears without error. I am speculating may be its the RAM problem
> (since its showed usage of RAM for > 86%), so I am thinking of transferring
> the calculations out on higher RAM machine. Any other ideas?
>
> Regards
> Monika
>
>
> On Fri, Mar 25, 2011 at 9:01 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > Hello,
> >
> > My comments are below:
> >
> > On Thu, Mar 24, 2011 at 8:09 PM, Monika Sharma <mondyn.gmail.com> wrote:
> >
> > >
> > > PBSA run went file and it created 3 heavy files for complex, receptor
> and
> > > ligand, totaling to about 4 GB. There is no error reported while
> > > calculation
> > > of values for each snapshot.
> > > This is an excerpt of complex output file
> > >
> >
> > [snip]
> >
> > TDC 2-> 2 0.000 -4.994 18.538 -78.942 1369.696
> > > TDC 2-> 3 0.000 -6.268 3.342 -28.524 -503.818
> > > TDC 2-> 4 0.000 -0.263 17.073 -16.884 0.000
> > > TDC 2-> 5 0.000 -0.031 11.360 -11.225 0.000
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > > and so on.........
> > >
> > > I am not able to understand why the first column is 0 (it is 0.000 for
> > > each
> > > snapshot of complex, receptor or ligand) and what is meant by that?
> > >
> >
> > The first column is the internal potential term (i.e. bond, angle, dihed,
> > etc.), and the 1-4 non-bonded terms are added to EEL and VDW (idecomp=4).
> > Therefore I wouldn't expect there to be any pairwise internal terms. I
> > would only expect pairwise non-bonded interactions to be accumulated
> here.
> >
> >
> > >
> > > The problem occurs while doing the statistics. It seems the program
> ends
> > > without error while reading the output files for complex.
> > >
> >
> > How do you know it has ended? 4 GB files are quite large and can take a
> > deceptively long time to parse. How long did it hang before you killed
> it?
> > Keep in mind that this is a perl script (interpreted language), which
> > parses
> > files much more slowly than a compiled language like C or Fortran.
> >
> > Hope this helps,
> > Jason
> >
> >
> > >
> > >
> >
> .................................................................................
> > > Calc contrib for ./snaps/snap_lig.crd.1999
> > > Calc MM/GB/SAS
> > > Calc contrib for ./snaps/snap_lig.crd.2000
> > > Calc MM/GB/SAS
> > >
> > > =>> Doing statistics
> > > =>> Reading input
> > > =>> Reordering files
> > > Final order:
> > > 1. snap_com.all.out: 1 - 71 72 - 72
> > > 2. snap_rec.all.out: 1 - 71
> > > 3. snap_lig.all.out: 72 - 72
> > > =>> Reading files
> > > Reading snap_com.all.out
> > >
> > > At this point the program exits without error. By this, I mean I cannot
> > see
> > > any pbsa command running on the machine using ps -A or top. I tried
> > > re-running the program twice for whole calculation itself, but with no
> > use.
> > >
> > > Please advise how to get out of this problem. I have patched the recent
> > > bugfixes for Amber10.
> > >
> > > Thanks in advance.
> > > Regards
> > > Monika
> > >
> > >
> > > --
> > > ((`_.[Monika]._))
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ((`_.[Monika]._))
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Mar 25 2011 - 04:30:02 PDT
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