Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Wed, 17 Dec 2014 09:58:28 -0800

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 - 10:00:03 PST