Re: [AMBER] Energy Calculation Problem

From: Sushil Mishra <>
Date: Tue, 22 Feb 2011 20:06:53 +0100

On Tue, Feb 22, 2011 at 5:33 PM, Nitu Bansal <>wrote:

> 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 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.
   Can you see the same distorted structure of the ligand in the trajectory
file ? Is this behavior coming from MD simulation or it happened during the
snapshot generation ?

> 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 - 11:30:11 PST
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