David and Jim,
Thanks. I am now using the ff94 charges.
However, the problem of two (reasonably different) conformations
minimizing into one, is still there.
Regards,
Sia Meshkat
-----Original Message-----
From: David A. Case [mailto:case.scripps.edu]
Sent: Monday, July 07, 2003 3:04 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:
>
> 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.?
There is no such beast. Charge distributions for non-polarizable force
fields are the same as in ff94.
Please see the files in $AMBERHOME/dat/leap/cmd, or pp. 17-19 of the
Users' Manual.
...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 - 23:53:01 PDT
