Hi George,
As a supplement to what Bill said, commas are not permissible in input
variables in the current release. The upcoming version does not suffer from
this limitation, so it will be easier to define masks then.
Another option is to pre-process your trajectory yourself, manually removing
all of the waters you don't want and keeping those that you do. Then just
set the strip_mdcrd variable to 0 to avoid stripping everything and just
supply your complex_prmtop, mdcrd, and receptor and ligand_prmtops.
Hope this helps,
Jason
On Tue, Feb 15, 2011 at 11:57 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> You will have to explicitly set the strip_mask variable in the MMPBSA.py
> input file. You will have to define the mask to strip out all the water
> molecules you do not want, but specifically keep the residue number of the
> one water molecule you want to keep. You can read about the details of how
> to define the residue masks in the manual.
>
> Good luck!
>
> -Bill
>
> On Tue, Feb 15, 2011 at 11:40 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
> > Hi everybody,
> >
> > I understand that MMPBSA.py strips all HOH molecules (?) and ions from
> the
> > original trajectory. In my case, an individual HOH molecule contributes
> to
> > the binding of the ligand to the receptor. This is in accordance with the
> > corresponding crystallographic model.
> >
> > Is there a way of keeping this HOH molecule in the trajectory files? I
> > would like to find out the contribution of this HOH molecule to delta G
> and
> > delta S.
> >
> > I'd be grateful for any advice on how to go about this issue.
> >
> > Best regards
> >
> > George
> >
> >
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 15 2011 - 09:30:02 PST
