On Thu, Oct 03, 2002, Michael Ford wrote:
>
>
> I was just wondering about thoughts anyone might have as to whether
> counterions neutralizing a ligand charge should be included with
> receptor or ligand in MM-PBSA type calculations. I have a negatively
> charged ligand, neutralized with a sodium counterion. I'm guessing I
> should throw it in with the receptor.
I generally recommend that mobile counterions be treated as a part of the
solvent: they are thrown away before the MM-PBSA calculations start.
Use the "saltcon" variable (for GB) or equivalent in your PB program to
include salt-dependent effects.
[Aside: note that if you use Delphi, you need to take care in doing PB
calculations with non-zero salt: the program's output can be confusing.]
..hope this helps...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Thu Oct 03 2002 - 13:43:35 PDT
