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

From: David Case <>
Date: Sat, 2 Feb 2019 17:14:53 +0000

On Sat, Feb 02, 2019, Qasim Pars wrote:
>I would calculate the hydration free energy of sodium ion (Na+) using the
>generalized Born approximation but I couldn't find the Van der Waals radii
>of Na+ in GAFF.

The Born approximation (as implemented in Amber) does not use van der
Waals radii, but rather "Born radii" (sometimes called "dielectric"
radii). Beyond that, Amber-based parameterizations assumes that mobile
ions like Na+ will be considered to as a part of the solvent (not the
solute), and hence will not need such radii.

Hence, there in fact is no "GAFF" dielectric radius for Na+. I'm
betting there are people reading this list that have played around with
simulations using explicit ions and implicit water, rather than the
more common treatment of both ions and water as implicit. They may be
able to chime in with parameters they have used.

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.

....good luck....dac

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Received on Sat Feb 02 2019 - 09:30:04 PST
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