Hi Dr. Jason
Thanks so much for your interest and sorry if I made any inconvenience.
I see the job has been stopped. But there was no any error in the strout or strerr files. I resubmitted it again many times without any hope.
Because all the calculations finished and the job stopped at the statistics part, so I run the statistics script using: ( 1 200 means from snap 1 to snap 200, is that right?)
mm_pbsa_statistics.pl 1 200 snapshot_statistics.in snapshot_statistics.out
=>> Reading input
=>> Reordering files
Final order:
1. snapshot_com.all.out: 1 - 226
2. snapshot_rec.all.out: 1 - 225
3. snapshot_lig.all.out: 226 - 226
=>> Reading files
Reading snapshot_com.all.out
Missing BOND for MM in 1 (residue 1)
Do you have any idea what the problem is? Unfortunately; we don't have amber11. Please, bear in your mind the calculation finished normally when I specified DC =1
I resubmitted the jobs again without decompostion to get the total binding energy.
Thanks in advance
Eliac
--- On Tue, 3/22/11, Jason Swails <jason.swails.gmail.com> wrote:
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] mmpbsa.pl energy decompistion stopped
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Tuesday, March 22, 2011, 1:24 AM
> Hello,
>
> On Mon, Mar 21, 2011 at 4:41 PM, Eliac Brown <eliacbrown.yahoo.com>
> wrote:
>
> >
> > In case of DCTYPE = 1, the calculation finished
> without any problem. But
> > defining DCTYPE = 3, the calculation stopped without
> complaining.
> >
>
> How do you know it failed?
>
>
> > Here is the end of the log file of MMPBSA.pl with
> DCTYPE=3
> > =>> Doing statistics
> > =>> Reading input
> > =>> Reordering files
> > Final order:
> > 1.
> snapshot_com.all.out: 1 - 226
> > 2.
> snapshot_rec.all.out: 1 - 225
> > 3.
> snapshot_lig.all.out: 226 - 226
> > =>> Reading files
> > Reading snapshot_com.all.out
> >
> > One more question, in the statistics.out file, I
> couldn't find the final
> > results and it is not printed in any ther files, so I
> sum all the numbers
> > under TGBTOT (in Delta section), is there any easy
> way?
> > Any suggestion would be appreciated.
> >
>
> As far as I know, the perl version of the script does not
> print out the
> final binding free energy numbers; just the
> decomposition. Furthermore,
> simply summing TGBTOT will not give you the total energy, I
> don't think.
> The issue that you have is that inter-residue, non-bonded
> interactions are
> included in both residues. You could write a small
> awk script to pull out
> the necessary values from the output files (if you kept
> them via the
> "verbose" keyword in the input file).
>
> If you have Amber11, MMPBSA.py provides decomposition
> functionality and
> prints out a decomp summary as well as a final binding
> energy summary as
> well. It also simplifies the input procedure (so it
> figures out recmap,
> ligmap, etc.).
>
> Hope this helps,
> Jason
>
> Thanks in advance
> > Eliac
> > P.S. All bugfix was applied.
> > P.S. I checked most of the pre-posted questions.
> >
> >
> >
> >
> > _______________________________________________
> > 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
>
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Received on Mon Mar 21 2011 - 20:00:02 PDT
