could u send 5-10 step long traj, corresponding prmtop file, and ff details
to us ?
On Wed, Feb 23, 2011 at 7:12 AM, Nitu Bansal <nitubansal1986.gmail.com>wrote:
> 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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> > > > > 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)
> > > _______________________________________________
> > > 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Feb 22 2011 - 23:00:03 PST
