Hi Ray,
Thank you for your suggestion about changing the dielectric constant of the
solute. I will definitely try this.
Since I am interested in determining relative binding free energies, only,
for a set of nucleotides, I believe it may be justified to ignore the
contributions from the phosphate atoms since these belong to all ligands
whose binding free energies are being compared. So I was thinking in terms
of going into the AMBER MMPB-SA code and introducing a parameter, similar
to what you have with residue decomposition, where the sum over atomic
sites involved in determining binding free energy is only taken over
selected atoms. Does this sound feasible to you?
Thanks,
Holly
On Wed, Dec 17, 2014 at 10:58 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Holly,
>
> I suppose you can't simply exclude any ligand atom in the calculation
> ... since you are not modeling the same system as measured in
> experiment.
>
> One common workaround in modeling highly charged ligands/active sites
> is to use a higher solute dielectric constant, at least 4. The vacuum
> value of 1 always causes problem in binding calculations.
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor,
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Tue, Dec 16, 2014 at 4:50 PM, Hallel Freedman <hfreedma.ualberta.ca>
> wrote:
> > I'm sorry - I meant to write "contributions from certain ligand atoms"
> > instead of "contributions from certain receptor atoms"
> >
> > Holly
> >
> > On Tue, Dec 16, 2014 at 5:49 PM, Hallel Freedman <hfreedma.ualberta.ca>
> > wrote:
> >
> >> Dear AMBER support,
> >>
> >> I was wondering if any of you have any suggestions for me about how to
> go
> >> about performing an MMGB-SA or MMPB-SA calculation in which
> contributions
> >> from certain receptor atoms are excluded. In particular I am looking at
> >> the binding of nucleotide analogs and I believe that my results have a
> lot
> >> of error associated with the high charge in the triphosphate groups;
> thus
> >> I would like to exclude the atoms in these groups from my calculations.
> >>
> >> Thanks,
> >> Holly
> >>
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Received on Wed Dec 17 2014 - 10:30:02 PST
