On Sat, Dec 14, 2002, jzhou wrote:
>
> My question is, given the coordinates of two atoms, could I decide whether
> they are bond or non-bond simply from their distance? Is their any empirical
> value to distinguish bond and non-bond pairs?
>
Force field programs generally use libraries or other mechanisms to encode
connectivity information. However, the following algorithm (taken from
the "makebonds()" routine in NAB, see the web page below) works pretty well:
For atoms a and b:
if either a or b is a hydrogen,
make a bond if the a-b distance is less than 1.20 Ang.
else
make a bond if the a-b distance is less than 1.85 Ang.
This is not guaranteed to work in every instance, but is *pretty* reliable,
and may help you get started.
..good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
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 | http://www.scripps.edu/case
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Received on Mon Dec 16 2002 - 17:56:29 PST
