AMBER Archive (2008)

Subject: Re: AMBER: Electrostatic Energy Components

From: Jojart Balazs (jojartb_at_pharm.u-szeged.hu)
Date: Sun Nov 23 2008 - 02:34:01 CST

Hi,
In the GAFF paper we can read the following:
"derive torsional angle potential Vi to reproduce the
ab initio rotational profile."
It means, based on my opinion, that that they derived the parameters to
obtain the ab initio torsional profile. (which is not good, because we
have to fit to the QM-MM profile).
Do I misunderstanding any or everything in the description in the paper?
Thank you for your help in advance!
Balazs Jojart

David A. Case írta:
> 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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