If you set strip_mdcrd=0, then MMPBSA.py will completely ignore the
strip_mask (default or otherwise) and keep everything that is in your
initially supplied trajectory (complex, water, metal, etc.). However, if you
leave strip_mdcrd=1 you can set the strip_mask to only the specific water
and metal residues you want to remove from the MM-PBSA calculation.
I hope this helps.
-Bill
On Tue, Oct 5, 2010 at 5:31 AM, William Flak <williamflak.yahoo.com> wrote:
> Dear Dr. Bill and Jason
> Thanks so much for your reply.
> But in case I used strip_mdcrd=0, it would retain the metal ion during
> mm-pbsa calculation, is that correct?
> or should I define only the strip_mask without including WAT?
> Thanks in advance
> W. Falk
>
> --- On Tue, 10/5/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> > From: Jason Swails <jason.swails.gmail.com>
> > Subject: Re: [AMBER] Water bridge - MMPBSA
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Date: Tuesday, October 5, 2010, 1:45 AM
> > 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
> > >
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Oct 05 2010 - 04:00:05 PDT
