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
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Received on Fri Oct 01 2010 - 07:30:03 PDT
