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
Received on Tue Oct 05 2010 - 03:00:03 PDT
