AMBER Archive (2006)

Subject: Re: AMBER: problem with amber 9 and igb=5

From: M. Scott Shell (shell_at_maxwell.compbio.ucsf.edu)
Date: Thu Jun 08 2006 - 11:05:10 CDT

Carlos Simmerling wrote:
> Scott,
> I don't see any obvious problems but have you tried it without the
> weight change?
>
> also unless this is just some test system I would really avoid using
> ff96 as it is
> quite bad, not just the (strong) beta bias but your glycine will
> almost certainly be
> very misbehaved. I would not use this combination and would have very
> serious reservations about any article that I read where it was used.
> We've also shown that igb1 and igb5 have a very strong alpha helical
> bias, and
> while the combination of gb and ff96 might sometimes seem to give
> secondary structure
> propensities in line with experiment it would be for all the wrong
> reasons.
> just my opinion... I really want people to stop using this parameter
> set. Even the
> Kollman lab where it was developed abandonded it very quickly.
> Carlos
>
>
I tried it without the weight change and without the DISANG line and the
problem still occurs.

I am very interested in your comments regarding ff96. We have performed
a number of force field tests and found this one to be the best, for the
time being, as a "middle of the road" parameter set for capturing both
alpha and beta motifs in short peptides. Many of the newer sets, like
ff99 and ff03, gave far-too-helical results for known stable hairpins.
This seems in line with Okamoto's recent work (the Yoda et al paper in
Chem Phys). Can you point me to some work on ff96 showing its
problems? Moreover, which implicit solvent/force field combination
within Amber would you recommend? We are constantly searching for the
best force field setup and are open to suggestions.

-Scott

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