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 "all_amino02.in".
Where can I get "all_amino99.in", etc.?
Thanks,
Sia Meshkat
-----Original Message-----
From: David A. Case [mailto:case.scripps.edu]
Sent: Monday, July 07, 2003 2:24 PM
To: Sia Meshkat
Cc: amber.heimdal.compchem.ucsf.edu
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
> (all_amino02.in). 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
polarization
turned on. But (to repeat the above) there has not yet been a lot of
testing
of ff02. My best guess would be that ff02EP is likely to be better than
ff02,
but that both will continue to have some of the phi-psi problems that
have
been noticed for other force fields that use parm94.dat or parm99.dat.
But this is a "guess", not an observation.
...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Mon Jul 07 2003 - 22:53:01 PDT
