Re: [AMBER] VdW parameters in AMBER

From: Andreas Gavrielides <>
Date: Thu, 9 Feb 2017 11:25:25 +0000

Dear Dr. Case,

Thank you very much for your very helpful and fast response it has been a huge help and a solution to my probl¨¦matique.

Kind regards,

Andreas Gavrielides

Andreas Gavrielides

Doctorant au CIRIMAT-INP Toulouse

SURF Equipe


 4 All??e Emile Monso BP 44362,

 31432 Toulouse Cedex 4

From: David Case <>
Sent: Wednesday, February 8, 2017 7:28 PM
To: AMBER Mailing List
Subject: Re: [AMBER] VdW parameters in AMBER

On Wed, Feb 08, 2017, Andreas Gavrielides wrote:
> I would like a clarification in regard to the pairwise parameters used
> in GAFF. For the sigma (¦Ò) values needed to calculate the LJ potential
> is it sufficient to just divide by 2^(1/6) or is it also mandatory to
> multiply by 2. Because if not multiplied by 2 the sigma parameters are
> too small and almost two times smaller than those in other AMBER force
> fields.

The values in the nonbonded lines of a parm.dat file are Rmin/2 and epsilon.
Rmin/2 is in Angstroms, epsilon is is kcal/mol

Rmin/2 = sigma*(2**1/6)/2 where "sigma" is a standard LJ sigma parameter.

This has nothing to do with gaff or gaff2: all Amber parameter files use
this format.

More info is here:

...hope this helps....dac

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