Re: a question about force field in AMBER

From: David A. Case <>
Date: Mon 16 Dec 2002 17:56:29 -0800

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.
          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:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Mon Dec 16 2002 - 17:56:29 PST
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