Re: AMBER: non-bonded cutoffs

From: David A. Case <>
Date: Fri, 26 Sep 2003 08:32:09 -0700

On Fri, Sep 26, 2003, Michael Dolan wrote:

> When a user specifies a non-bonded cutoff of 8.0A around an atom in a
> protein, are a) only atoms within the 8.0A radius included in the
> calculation, or b) atoms within 8.0A plus those atoms which are part of
> a residue having at least one atom within the 8.0A included?

This depends on what version you are using. Sander in versions 6 and 7
uses an atom-based cutoff (your option "a"); in versions 5 and earlier, a
residue based cutoff (your option "b") was used. Think sander_classic
uses a residue-based cutoff as well.


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:                   
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Received on Fri Sep 26 2003 - 16:53:01 PDT
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