Re: [AMBER] vdw radii of sodium ion in GAFF

From: Thomas Cheatham <>
Date: Sat, 2 Feb 2019 11:31:25 -0700 (MST)

> Of course, you can (and perhaps should, depending on what you wish to
> do) just use a Na+ radius that gives the known (experimental) hydration
> free energy.

Yes, this is what we've done in the past when explicit ions want to be
included. The closest command in CPPTRAJ is applied to save the closest
"n" ions where n is up to your choice... GB/PB calculations were applied
on a single Na+ adjusting radii to get the hydration free energy. Then
this radii used in the MM-PB/GBSA calculations.

Two papers included a limited set of water or ions:

Stefl et al. Biophysical J. 85, 1787-1804 (2003)
  * includes Na+ ions in or near the G-DNA channel

Spackova et al. JACS 125, 1759-1769 (2003)
  * includes explicit water and does both single vs. separate trajectory
    approaches with MM-PBSA


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Received on Sat Feb 02 2019 - 11:00:02 PST
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