AMBER Archive (2009)

Subject: Re: [AMBER] force fields

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Wed Apr 15 2009 - 07:43:49 CDT

On Wed, Apr 8, 2009 at 8:23 PM, Mark M Huntress wrote:
> when I load
> leaprc.ff03
> and then later load
> leaprc.gaff
>
> the ff03 stays loaded, and both can work together. Am I correct about that?

Hi Mark,

Your question has already been answered by Ross, but I just wanted to
add a warning here: Notice that the GAFF force field uses either
HF/6-31G* RESP charges in the derivation, or AM1/BCC charges, which
are parameterized to reproduce the former. What that means is that the
GAFF force field is better suited to be used with a force field like
ff99SB, which uses the same charge model. ff03 derives the charges
from a B3LYP/cc-pVTZ//HF/6-31G** calculation, so they *may* not be as
compatible with GAFF.

See:
1. GAFF: Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case,
D. A. J. Comput. Chem. 2004, 25, 1157-1174.
2. FF03: Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.;
Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.;
Wang, J.; Kollman, P. J. Comput. Chem. 2003, 24, 1999-2012.
3. 99SB: Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.;
Simmerling, C. Proteins: Struct., Funct., Bioinform. 2006, 65,
712-725.

Gustavo.

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