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

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 24 Mar 2011 20:31:44 -0700

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
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Received on Thu Mar 24 2011 - 21:00:02 PDT
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