RE: Valdiation of Latest Amber parameters

From: Sia Meshkat <>
Date: Mon, 7 Jul 2003 14:48:41 -0700

Thanks for the quick response.

Actually, I am trying to run without polarization with parm99.dat, but
the only charge data I can find for amino acids is in "".

Where can I get "", etc.?

Sia Meshkat

-----Original Message-----
From: David A. Case []
Sent: Monday, July 07, 2003 2:24 PM
To: Sia Meshkat
Subject: Re: Valdiation of Latest Amber parameters

On Mon, Jul 07, 2003, Sia Meshkat wrote:

> Are there any papers or data available on the results of the latest
> Amber parameters for simple peptides?

Not as far as I am aware.

> I have attached two conformations of Alanine Tetrapeptide from the
> frequently cited Beechy et al paper in JACS 1997-119.
> In the following experiment, I minimized the potential energy of these
> two conformations using the parm99.dat parameters + 2002 charges
> ( As a result of energy minimization, both
> conformations converge to a single conformation. In earlier Amber
> parameter sets, such as ff94, these two conformations remain distinct,
> when minimized.

Just to be sure: you should only use the above parameters with
turned on. But (to repeat the above) there has not yet been a lot of
of ff02. My best guess would be that ff02EP is likely to be better than
but that both will continue to have some of the phi-psi problems that
been noticed for other force fields that use parm94.dat or parm99.dat.
But this is a "guess", not an observation.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Mon Jul 07 2003 - 22:53:01 PDT
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