AMBER Archive (2004)

Subject: Re: AMBER: how to correctly change frcmod?

From: David A. Case (case_at_scripps.edu)
Date: Sun Jan 25 2004 - 19:17:47 CST

On Fri, Jan 23, 2004, opitz_at_che.udel.edu wrote:
>
> I am just beginning to use Amber 7. I am trying to simulate a dendrimer
> whose pdb file I already have. This pdb file contains all atoms, except
> the hydrogens, as those gave me problems. After removing the hydrogens
> from my pdb file, antechamber accepted the file ....

This is wrong; you have to keep the hydrogens for antechamber to work as
desired. Also, atom names within a residue must be unique; you example
has many "C1" carbons, for example. These have to all become unique.

> > mods = loadamberparams frcmod
> Loading parameters: ./frcmod
> Reading force field mod type file (frcmod)
> Unknown keyword:
> in parameter file.
> Unknown keyword:
> in parameter file.
>
> Does anybody know what causes this?

I don't see a problem in the file you sent. You might try increasing the
verbosity level to get a better hint.

..good luck..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:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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