Hello,
Another option is to pre-process the trajectory using ptraj using the
"closest" command and use the "strip_mdcrd=0" option. If the bridging water
exchanges during the simulation, this is really the only way to do this.
Don't forget that you need to create an prmtop file that has 1 water
molecule.
Good luck!
Jason
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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Oct 04 2010 - 19:00:04 PDT
