Are you sure that the top files created for the ligand is correct and there
were no warning or error by leap. Just to be sure, u have to have the input
top file of complex, rec and ligand without water. I would write a PDB
(using ptraj) of the complex using top and traj file from MD simulation,
strip the water, and make PDB of complex. Copy the rec and ligand part
in separate files. Now create top file file for each one, (com, rec,lig) and
use them as input file in the mm_pbsa.pl, where and NTOT will the the total
number of atoms (including water) in traj file from MD simulation.
Hope it helps.
On Wed, Feb 23, 2011 at 5:54 AM, Nitu Bansal <nitubansal1986.gmail.com>wrote:
> 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
>
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Received on Tue Feb 22 2011 - 22:00:05 PST
