AMBER Archive (2003)

Subject: RE: Valdiation of Latest Amber parameters

From: caldwell_at_heimdal.compchem.ucsf.edu
Date: Mon Jul 07 2003 - 16:44:53 CDT

The charges are the same for parm94 parm96 and parm99,
use all_amino94.in

jim

On Mon, 7 Jul 2003, Sia Meshkat wrote:

> 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
>
> 

-- 

----------------------------------------------------------------------------
NOTE NEW MAILING ADDRESS & FAX NUMBER:

James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-514-3866  
UCSF Box 2240                             (email) caldwell_at_heimdal.ucsf.edu
600 16th Street
University of California
San Francisco, CA 94143-2240
----------------------------------------------------------------------------