AMBER Archive (2008)

Subject: Re: AMBER: to understand GAFF: about A and B coefficients

From: David A. Case (case_at_scripps.edu)
Date: Tue Jun 17 2008 - 11:52:41 CDT

On Tue, Jun 17, 2008, Alan wrote:
>
> %FLAG LENNARD_JONES_ACOEF
>
> %FORMAT(5E16.8)
>
> 5.71629601E+03 7.62451550E+04 8.19971662E+05
> %FLAG LENNARD_JONES_BCOEF
>
> %FORMAT(5E16.8)
>
> 1.85196588E+01 1.04660679E+02 5.31102864E+02
>
> I see values for coef. A and B. However, in amber10/dat/leap/parm/gaff.dat
> what one sees is (radius in Ang. and pot. well depth in kcal/mol):
> ha 1.4590 0.0150
> ca 1.9080 0.0860
>
> I know there's a relation between those values, but I couldn't deduce or
> find it in amber manuals.

http://ambermd.org/Questions/vdwequation.pdf

...dac

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