AMBER Archive (2009)

Subject: Re: [AMBER] only ff94 and ff99 for GBSA?

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Jul 28 2009 - 02:32:52 CDT

Dear Andrew,

> Amber ff99SB field still has the same partial scheme from Amber99,
> right? And this partial charges scheme is different from amber03,
> so I'm a bit confused about choice of the force field for proteins
> molecular dynamics.

charges of ff99SB (Hornak et al.) are these from ff99 (Amber99, Wang
et al.)/Amber98/Amber96 and Amber94 (Cornell et al.)

charges of ff03 are derive using a different approach to ff94.

Consequently, you have two different FF for proteins in the Amber 10
distribution. You will have to choose between one of these two.

regards, Francois

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