On Wed, Apr 3, 2013 at 10:26 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> 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.
>
Don't forget to modify "strip_mask" if you want to keep some water
molecules. By default all waters (and ions) are stripped from the solvated
trajectory.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Apr 03 2013 - 08:00:02 PDT
