Hi
I have already followed the same procedure but the problem still exists.
Thanks
On Wed, Feb 23, 2011 at 11:08 AM, Sushil Mishra <sushilbioinfo.gmail.com>wrote:
> 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)
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> > >
> >
> >
> >
> > --
> > 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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--
Nitu Bansal
M.S Pharm
Research Scholar
Department of Pharmacoinformatics
S.A.S Nagar NIPER Mohali (Chandigarh)
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Received on Tue Feb 22 2011 - 22:30:04 PST
