Re: mm_pbsa

From: David A. Case <>
Date: Mon 23 Sep 2002 06:25:02 -0700

On Sun, Sep 22, 2002, Mahadevan Seetharaman wrote:
> I was having exactly the same problem. Does that mean Na+ and K+ ions have
> not been parameterzed for mm_pbsa? Is there an alternative, other then
> changing the code?

Yes, that is what it means. My personal feeling is that sodium and potassium
ions in solution should be considered as part of the solvent, and hence be
stripped away, along with the waters, before running mm_pbsa. Use the saltcon
variable (in GB, or the equivalent in PB) to estimate the effects of mobile
co- and counterions.

If you do want to make these ions part of the solute, you could probably use
ionic radii from PB calculations that in the literature for them. But I'd
at least recommend then comparing the two ways of doing things. For one
thing, the amount of sampling you will need to do to explicitly average over
all of the ion positions is often considerably greater than the amount of
sampling needed to average over just the atoms of the "real" solute.

..hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Mon Sep 23 2002 - 06:25:02 PDT
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