Re: [AMBER] Difference in PB results of mmpbsa and mmpbsa.mpi

From: Bill Miller III <brmilleriii.gmail.com>
Date: Fri, 11 May 2012 08:14:47 -0400

I would suggest upgrading to AmberTools12 and using those MMPBSA.py and
MMPBSA.py.MPI scripts. I don't think you should have this problem with
AmberTools12. Although, if you still have this issue, it will be easier to
diagnose if you have the most recent release.

-Bill

On Fri, May 11, 2012 at 5:52 AM, <amin.imtech.res.in> wrote:

> Dear all, I am trying to calculate the binding energy of a protein ligand
> complex using MMPBSA from AmberTools 1.5. I find that while the GB results
> are
> almost same for both MMPBSA and MMPBSA.MPI there is significant difference
> in in
> PB values. I am using 25 processors for MMPBSA.MPI. I am using the exact
> same
> script for both. I found a similar problem in archives and thus applied the
> suggested patches. However I still have the problem. Here are the results:
> MMPBSA:GB: Delta Total = -38.6156
> PB: Delta Total = -50.4641
>
> MMPBSA.MPI:GB: Delta Total = -36.4499
> PB: Delta Total = -18.5299
>
> I find that the main difference is arising due to G SOLV of ligand (-4.8 vs
> -50.02).
> Can someone please help me with this?
> Amin.
>
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-- 
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri May 11 2012 - 05:30:05 PDT
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