AMBER Archive (2003)

Subject: Re: AMBER: non-zero 10-12 coefficient

From: David A. Case (case_at_scripps.edu)
Date: Sat Dec 13 2003 - 14:48:12 CST

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outdated, just that you have to recompile sander as indicated in order to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 

-- 

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David A. Case                     |  e-mail:      case_at_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:                   
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