The VDW energy term has to be coming from somewhere, and the explanation is
hidden somewhere in your files. Make sure you're checking the
_MMPBSA_*.mdcrd files with the prmtop files you provided to make sure that
the trajectories are being properly formed, and see if you can locate any
steric clashes there (don't just look at your input files). All the MM/PBSA
scripts do (regardless of version) is automate the process of using sander
to extract potential terms and calculating the statistics at the end, so if
something goes wrong you may have to look at the steps that the script takes
to make sure it didn't mess up somewhere.
Good luck!
Jason
On Fri, Oct 1, 2010 at 10:20 AM, Senthil Natesan <sen.natesan.yahoo.com>wrote:
> Jason,
>
> I used the same trajectory file for my previous calculation. The only
> difference
> is
> the unsolvated complex prmtop file. The previous calculation gave me
> sensible
> energy
> values.
> I am attaching the output file for the previous calculation here..
>
> I made pdb file from the above unsolvated prmtop and inpcrd and it seems
> fine,
> there are
> no obvious steric clash any where.
>
> thanks,
>
> Senthil
>
>
>
>
>
>
>
> ________________________________
> From: Jason Swails <jason.swails.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Fri, October 1, 2010 9:47:36 AM
> Subject: Re: [AMBER] MMPBSA.py - very high energy terms
>
> Hello,
>
> Your VDW terms are too high, implying some type of steric clash. Study the
> output files (_MMPBSA_complex_gb.mdout, or something of the like) and
> visualize the generated trajectories with your prmtops to see if you can
> locate where this clash is taking place. This may give you some hint as to
> how to fix it.
>
> Good luck!
> Jason
>
> On Fri, Oct 1, 2010 at 9:27 AM, Senthil Natesan <sen.natesan.yahoo.com
> >wrote:
>
> > Hi Jason,
> >
> > As I already mentioned, I used "unsolvated complex prmtop" from different
> > step
> > and there was warnings indicating the inconsistencies.
> > Now I prepared the above file from the same step as I prepared protein
> and
> > ligand prmtop,
> > and ran MMPBSA.py. This time, there was no warnings and calculations went
> > fine,
> > but the energy terms seem very very high.
> >
> > I once again, ran the calculations, with old unsolvated complex prmtop
> and
> > calculations seem
> > fine except those warnings.
> >
> > I am not sure whats going wrong. Any help would be appreciated.
> > Herewith I am attaching the final result from high energy run.
> > Thanks,
> >
> > Senthil
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Oct 01 2010 - 08:00:03 PDT
