Hi
During MD simulation, there was no distortion. Ligand went distortion during
snapshot extraction.
On Wed, Feb 23, 2011 at 12:36 AM, Sushil Mishra <sushilbioinfo.gmail.com>wrote:
> On Tue, Feb 22, 2011 at 5:33 PM, Nitu Bansal <nitubansal1986.gmail.com
> >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 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.
> >
> 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)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Nitu Bansal
M.S Pharm
Research Scholar
Department of Pharmacoinformatics
S.A.S Nagar NIPER Mohali (Chandigarh)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 22 2011 - 21:00:03 PST
