Are you using the python (MMPBSA.py) or perl (mm_pbsa.pl) script to
calculate MM-PBSA? If you are using MMPBSA.py, you can just set the
strip_mask variable to all the other water residues except the one that
makes a water bridge in the active site. This will override the default
strip_mask as described in the Amber 11 manual.
Good luck!
-Bill
On Mon, Oct 4, 2010 at 6:25 PM, William Flak <williamflak.yahoo.com> wrote:
> Dear AMBER
> During MM-PBSA, water molecules were striped out, according to the script.
> In fact, I was wondering, what is the case if there is a water molecule
> makes a bridge between the ligand and the active site.
> Should I rename it to something else except WAT and define in prmtop file,
> to keep it in MM-PBSA calculation?
> Any kind of help would be appreciated.
> Thanks in advance
> W. Flak
>
>
>
>
>
>
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Mon Oct 04 2010 - 16:00:04 PDT
