AMBER Archive (2004)

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

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

On Fri, Apr 16, 2004, anshul_at_imtech.res.in 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
one.

...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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