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.
>
> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> पिन कोड/PIN CODE :160036
> दूरभाष/EPABX :0172 6665 201-202
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 11 2012 - 05:30:05 PDT
