Yes, you will need to create a receptor prmtop file that is the receptor
plus two water molecules in order to do MM-PBSA with the water molecules
included.
-Bill
On Wed, Oct 6, 2010 at 3:46 PM, William Flak <williamflak.yahoo.com> wrote:
> Dear All
> Thanks so much for your reply.
> I have set initial_traj=1 and stripped ions out of the trajectories, as
> well, I used closestwater command to keep only the closest two water
> molecules that act as a bridge between the ligand and the receptor.
> I recreated a prmtop file for the complex (receptor+ligand+water). But I
> was wondering, what about receptor prmtop file, it should have the two water
> molecules too?
> Thanks in advance
> W. Flak
>
>
> --- On Tue, 10/5/10, Bill Miller III <brmilleriii.gmail.com> wrote:
>
> > From: Bill Miller III <brmilleriii.gmail.com>
> > Subject: Re: [AMBER] Water bridge - MMPBSA
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Date: Tuesday, October 5, 2010, 10:39 AM
> > 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
> > _______________________________________________
> > 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 06 2010 - 13:30:03 PDT
