Hi George,
On Tue, Feb 15, 2011 at 12:45 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Thanks Jason / Bill
>
> Your answers generated a couple of additional questions
>
> 1. Re Bill's answer
>
> I assume that I would have to set the strip_mask to remove all waters but
> the one that I'm interested in. Looking at the manual I fail to see what is
> the syntax for this operation. My molecular viewer shows that the HOH in
> question is numbered as molecule 2952.
>
> Would a syntax like the one below work?
>
> Input file for running PB and GB
> &general
> endframe=50, verbose=1,
> strip_mask=WAT2952
> # entropy=1,
>
This will not work. I actually suggest that you preprocess your trajectory
and use strip_mdcrd = 0 (and not let MMPBSA.py strip the solvent from your
trajectory). Typically, water exchange causes the *number* of the important
water molecule to change. If this is not the case (and no such exchange
occurs), then you can use a simple mask like ":401-2951,2953-8000" where
your solute has 400 residues and you have 8000 residues total (adjust those
numbers for your system obviously). Note that you have to use this mask in
ptraj; not MMPBSA.py since it doesn't allow commas. If water exchange does
occur, you'll have to use the "closest" or "closestwater" command in ptraj
to keep the one that is always in the right location.
Don't forget to create a complex/receptor/ligand prmtop with the water
molecule in the right place! MMPBSA.py should properly assign the masks if
you create your prmtop files properly and the ligand residues are continuous
(i.e. it's not residue 1 and 401 in the complex prmtop).
Good luck!
Jason
/
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
>
> 2. Re jason's answer
>
> Am I correct to assume that you mean that I need to strip manually the
> solvated_prmtop from all waters and ions except my water of interest? If
> this is the case, how does one work the numbering, e.g. identify the atoms
> of HOH 2952?
>
> Apologies if the above is trivial but I'm relatively inexperienced.
>
> Best regards
>
> George
>
>
>
> On Feb 15, 2011, at 6:03 PM, Jason Swails wrote:
>
> > 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
> >>>
> >>>
> >>> _______________________________________________
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> >>> 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
> > _______________________________________________
> > 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
>
--
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 - 11:30:04 PST
