AMBER Archive (2004)

Subject: Re: AMBER: TI, angle parameters for nitrogen, frcmod

From: David A. Case (case_at_scripps.edu)
Date: Thu Feb 05 2004 - 11:51:39 CST

On Mon, Feb 02, 2004, Carsten Detering wrote:

> *** Improper torsion parameters missing ***
> atom names: NB-C31-CA1-NA
> atom types: nb-c3-ca-n =pert=> nb-n3-ca-n
> Please add a dummy parameter of multiplicity 2
> for the pert types to your parameter set.
> - e.g. nb-n3-ca-n 0.0 0. 2.
> (This is because multiple torsional potentials may apply to a
> single torsion, and each is perturbed individually in gibbs.)
>
> How can I avoid this message, respectively how would I have to edit the
> frcmod file? I noticed that the format is
>
> n-ca-n3-DH 1 0.0 0. 2.
>
> but that the "1" is missing in the suggested dummy parameter.

You don't say what you tried, or what happened. There are examples of
frcmod files in $AMBERHOME/dat/leap/parm. The plastocyanin tutorial on the
web also has an example. Maybe these will help.

..dac 

-- 

==================================================================
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:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu