AMBER Archive (2004)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Feb 06 2004 - 06:58:45 CST

Okur, A., Strockbine, B., Hornak, V. and Simmerling, C., 'Using PC Clusters
to Evaluate the Transferability of Molecular Mechanics Force Fields for
Proteins", J. Comput. Chem., 24:21, 2003.

----- Original Message -----
From: "Wayne Dawson" <dawson_at_nih.go.jp>
To: <amber_at_scripps.edu>
Sent: Friday, February 06, 2004 2:50 AM
Subject: Re: AMBER: questions parm94/99 ff secondary structure

>
> 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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