AMBER Archive (2004)

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

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

On Fri, Jan 23, 2004, 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


================================================================== David A. Case | e-mail: 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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to