AMBER Archive (2008)

Subject: Re: AMBER: Electrostatic Energy Components

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Nov 22 2008 - 14:37:51 CST

On Sat, Nov 22, 2008, Jojart Balazs wrote:

>
> Based on this, and on our previous mailing with Junmei, we think that
> they made a mistake in the parameter fitting during the development of
> the GAFF forcefield. He used only the QM profile, and not the 'QM-MM_1'
> profile. Is this mean that the torsional parameters were obtained not in
> the correct way?

I think Junmei's parmscan program does the correct thing. Take a look at Fig.
3 in the gaff paper:

%A J. Wang
%A R.M. Wolf
%A J.W. Caldwell
%A P.A. Kollman
%A D.A. Case
%T Development and testing of a general Amber force field
%J J. Comput. Chem.
%V 25
%P 1157-1174
%D 2004

The full gaff result is plotted against the full QM result. The torsion-only
term here (a V2 term with a barrier of 1.2 kcal) has both a smaller barrier
and a different shape (with maxima at +/-90) than the full potential. So, the
"dihedral" term is clearly being added to the steric and electrostatic terms
before the comparison to QM is made.

...dac

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