We also encountered something similar, where we wanted to examine pKas as a
function of Mg2+ and/or Na+ binding (also as a function of the bulk
concentrations). The solution was to use MM/3D-RISM in place of MM/GBSA.
This is considerably more expensive, but pretty tractable if you have the
right resources. The radius selection problem for Mg2+ is replaced by the
problem of choosing LJ parameters, which is not a particularly solved
problem either, but can at least be rationalized based on explicit solvent
simulations.
HTH,
Brian
On Mon, Dec 12, 2016 at 10:52 AM, Ray Luo <rluo.uci.edu> wrote:
> Hi Francesco,
>
> We met something similar in a recent study for the human purinergic
> platelet receptor (J. Phys. Chem. B, 2016, 120 (48), pp 12293–12304).
> Indeed, different approaches used to model Mg++ do noticeably impact
> the agreement with experimental data.
>
> 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 Sun, Dec 11, 2016 at 11:44 PM, Francesco Gentile
> <fgentile.ualberta.ca> wrote:
> > Hello,
> > I am running free energy calculations on a series of protein-ligand
> > complexes. The ligands are all interacting with a magnesium ion in the
> > active site of the enzyme. How should I treat the magnesium ion (part of
> > the receptor, the ligand or what else?)? Also, does someone has
> experience
> > with this kind of situation and maybe can help me in setting up correctly
> > the calculation? Thanks in advance
> >
> > --
> > Francesco Gentile
> > PhD Student, Biophysics
> > CCIS 3-215, Department of Physics
> > 7-112, Li Ka Shing Centre for Health Research Innovation
> > University of Alberta, Edmonton, AB T6G 2E1
> > Canada
> > _______________________________________________
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>
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--
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak.anl.gov
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Received on Mon Dec 12 2016 - 09:30:03 PST
