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
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> _______________________________________________
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> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> >
> >
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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 Wed Oct 06 2010 - 13:00:04 PDT
