AMBER Archive (2004)

Subject: Re: AMBER: questions parm94/99 ff secondary structure

From: Wayne Dawson (dawson_at_nih.go.jp)
Date: Fri Feb 06 2004 - 01:50:07 CST

Carlos Simmerling wrote:
> if you are using parm94 or parm99, formation
> of helix may indicate a force field problem.
> this has been documented in the literature, check the
> amber archives.

Aini wrote:

> Thank you for your answer. However it is not clear for me. Can you
> give more details? I tried to search through amber archives and
> found out nothing because of lack of proper keywords.

I'm wonder the same thing now. It also does not seem to be clearly
stated within any abstracts at NCBI either.

As far as I can tell, parm99's agreement with the NMR data I've had to
fight with is not too bad. Parm94 is definitely poorer, although it is
more like it tends to form coil too readily. There are some things I
perhaps feel a _little_ suspicious about, but nothing has tipped me
off that the parm99 ff is seriously wrong. Obviously its far from
perfect, but who achieves perfection in science --- the ongoing saga
where we all stay tuned for the next installment? We've all sinned
and fallen way short of that one.

Do you have any references? Surely, I would regret ignoring such data
in my interpretations and comments.

Thanks
Wayne

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