Re: [AMBER] Question about Parmbsc1 Force Field

From: David A Case <>
Date: Sat, 3 Mar 2018 08:59:36 -0500

On Fri, Mar 02, 2018, Dan Gil wrote:
> I am simply searching for where someone got these numbers for the 12-6
> parameters of Na+ and Cl-:
> | sigma (nm) epsilon (kJ/mol)
> Cl 4.40104e-01 4.18400e-01
> Na 2.58400e-01 4.18400e-01
> This was included into a force-field set in GROMACS with parmbsc1 for the
> DNA.

This sounds like a question for the GROMACS list, but it might help to know
which water model you are using: ion parameters usually are coupled to a
particular water model (since the first shell of ligands around sodium and
bromide are usually waters.)

To compare with Amber parameters, remember that we measure epsilon in kcal/mol
(so you eps values above are 0.1 kcal/mol), and report Rmin = (sigma *
2**1/6)/2. So, Rmin for Na+ above is 1.45 Ang. I don't immediately see any
Amber parameters that look like that, but we have tons of choices....

You can get all the Amber parameters files by downloading AmberTools17 and
looking in the amber16/dat/leap directory tree.


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Received on Sat Mar 03 2018 - 06:30:02 PST
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