AMBER Archive (2004)

Subject: Re: AMBER: distance measurement in carnal and ptraj

From: David A. Case (
Date: Fri Apr 16 2004 - 10:46:04 CDT

On Fri, Apr 16, 2004, wrote:

> I was trying to measure the distance between hydrogen bond acceptor and
> donor in an alpha helical decapeptide using carnal, but the results i
> got were far from reality. This distance (between the Nitrogen of first
> residue and Oxygen of fifth residue) should be around 3.3 angstroms

No, it's the other way around: you want to look at the distance from the
N of residue 5 to O of residue 1 (for example) in an alpha helix. Using
a visualization program can be a big help in sorting out problems like this



================================================================== 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