AMBER Archive (2004)

Subject: Re: AMBER: saveamberparm warning in leap?

From: David A. Case (
Date: Mon Feb 16 2004 - 19:04:17 CST

On Mon, Feb 16, 2004, wrote:
> WARNING: There is a bond of 125.626000 angstroms between:
> ----------- .R<UNK 1>.A<N70 998> and .R<UNK 1>.A<C17 999>

> My question is, are warnings like these commonly seen? Do I have to be
> worried about them, and what do I have to do about them to make them
> dissapear?

You should worry about a 125 Angstrom(!) distance between two atoms that
are supposed to be bonded.

Is there supposed to be a bond between N70 and C17? If so, you have problems
with the coordinates; if not, you have problems with the prep file. It's
hard to be more specific given the information provided.

Note that the antechamber suite was never intended to work wtih molecules
containing thousands of atoms. Is there any way you can break your
molecule into pieces (residues, or the like), and use antechamber to get
parameters for the individual pieces, then link them together later?

...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