[AMBER] Energy Calculation Problem

From: Nitu Bansal <nitubansal1986.gmail.com>
Date: Tue, 22 Feb 2011 22:03:07 +0530

Hi Amber Community

I have found some problems with the use the mmpbsa with my molecule. I'm
trying to evaluate the PBTOT, GBTOT of these ligand into specific protein
receptor. I have the experimental values of
inhibition of these molecules and trying to find a theoretical reasons
for the observed experimental values, a correlation between them. I did the
minimization, heating and equilibration steps, plus two
nanoseconds of production step. I checked the mdcrd file in VMD at each
step. And no change in the protein structure was found. After
the extraction of snapshots, I calculated energy using MMPBSA.pl. The
internal energy and the van der Waal energy of ligand was very high .Then i
checked the one of the extracted snapshot of ligand in the VMD. The ligand
went distortion during extraction.

Please help me out.

Thanks for your suggestions.

Nitu Bansal
M.S Pharm III Sem
Research Scholar
Department of Pharmacoinformatics
S.A.S Nagar NIPER Mohali (Chandigarh)
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Received on Tue Feb 22 2011 - 09:00:04 PST
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