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

From: Monika Sharma <mondyn.gmail.com>
Date: Fri, 25 Mar 2011 15:48:59 +0530

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
Received on Fri Mar 25 2011 - 03:30:02 PDT
Custom Search