AMBER Archive (2004)

Subject: Re: AMBER: problem with frcmod file

From: David A. Case (case_at_scripps.edu)
Date: Mon Feb 23 2004 - 16:43:59 CST

On Mon, Feb 23, 2004, donna j wrote:
>
>
> Iam new in Amber nad iam trying to generate to run leap with cysteine -ve
> attached to zinc.This is the forcefield file i generated.when i run tleap
> iam getting the following error.Can somebody help me with this error.

First, make sure you can run simple simulations before you try modified
residues.

Second, you mail program may have mangled your frcmod file beyond
recognition, but remember the following points:

   You must have a title card in the frcmod file;
   There must be a blank line at the end of each section (e.g. the MASS,
     BOND, etc sections)
   Spaces are important; see the parm.dat files for the proper columns
     to use

Take a look at the example frcmod files in amber7/dat/leap/parm.

> frcmod file
> MASS
> SH 32.06
> ZN 65.37
> BOND
> ZN-SH 81.820 2.293
> ANGLE
> ZN-SH-C 18.92 111.6
> SH-ZN-SH 49.62 146.5
> DIHE
> C-SH-ZN-SH 9 0.0167 0.00 2.000
> C-C-SH-ZN 1 0.0909 0.00 3.000
> NONB
> ZN 1.95 0.25
> SG 3.00 0.063
>
...good luck...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
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