AMBER Archive (2003)

Subject: RE: Valdiation of Latest Amber parameters

From: Sia Meshkat (sMeshkat_at_proteinMechanics.com)
Date: Mon Jul 07 2003 - 16:48:41 CDT

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_at_scripps.edu]
Sent: Monday, July 07, 2003 2:24 PM
To: Sia Meshkat
Cc: amber_at_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 

-- 

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