Re: AMBER: distance measurement in carnal and ptraj

From: David A. Case <>
Date: Fri, 16 Apr 2004 08:46:04 -0700

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            |
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Received on Fri Apr 16 2004 - 16:53:01 PDT
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