By default, MMPBSA.py will remove all water residues from the trajectory
prior to performing any free energy calculations. So if you expected those
waters to be included in your calculations (i.e. if they were in your
receptor or ligand topology files), then there would have been an atom
mismatch between your topology files and the MMPBSA.py trajectory files,
which would explain your results. You may need to specify exactly which
residues should be removed to make the complex, receptor, and ligand
trajectories using the input variables for receptor and ligand masks if you
are going to include those water molecules in your calculations.
-Bill
On Wed, Apr 3, 2013 at 10:08 AM, Albert <mailmd2011.gmail.com> wrote:
> IC.
>
> thanks a lot for this helpful advices.
> There is some crystal waters in the input protein, probably they are not
> handle correctly? I will check it .
>
>
> best
> Albert
>
>
> On 04/03/2013 04:00 PM, Bill Miller III wrote:
> > This could be due to a mismatch between the topology files that you
> > provided and the trajectories created by MMPBSA.py from your original
> > trajectory. You should try visualizing the trajectories made by MMPBSA.py
> > with their corresponding topology files that you provided to see if they
> > look right. If they do not, it is likely because there is some mismatch
> > between the residues in the topology files, possibly ions or other
> residues
> > that were unintentionally removed? You can also check the mdout files
> > created by MMPBSA.py to see if they provide any helpful messages.
> >
> > -Bill
>
>
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--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-846-1633
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Received on Wed Apr 03 2013 - 07:30:04 PDT
