On Sat, Dec 13, 2003, Bimo Ario Tejo wrote:
>
> I tried to do a sander simulation (minimization, heating, equilibration,
> production) of a glycoprotein using Amber7 with parameter files taken from
> Robert Woods' group (http://glycam.ccrc.uga.edu/glycam/glycam_parameters.html):
> resp 010 and glycam_2000a.dat. The .lib files of sugar groups and prmtop and
> prmcrd were prepared using xleap -f leaprc.ff99.
>
> However, the simulation was stopped at minimization stage with this error
> message in output file:
>
> Found a non-zero 10-12 coefficient, but source
> was not compiled with -DHAS_10_12.
> If you are using a pre-1994 force field, you
> will need to re-compile with this flag.
>
> I dont think I'm using a pre-1994 ff. Does anyone have some experience how
> to use glycam ff in Amber7?
Glycam uses non-zero 10-12 terms, so you have to compile sander with
-DHAS_10_12, as the message indicates. As I understand it, this force field
"really" had its origins in about 1993, that is before the Amber protein
force fields removed the 10-12 terms. This does not mean is it is bad or
outdated, just that you have to recompile sander as indicated in order to
use it.
...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
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Received on Wed Jan 14 2004 - 15:53:08 PST
