Re: [AMBER] bondbydiatance

From: Jason Swails <>
Date: Mon, 6 Jan 2014 16:38:07 -0500

On Mon, Jan 6, 2014 at 12:42 PM, Sourav Purohit <> wrote:

> (The last mail had some error.)
> I applied bondbydistance command to a molecule many times independently
> with default cut-off value. In the first trial leap recognised 279 (111 non
> H-H) potential bond pairs. In the second it recognised 277 (109 non H-H)
> and in the third trial it was 278 (110 non H-H).
> Shouldn't the number of potential bond pairs be the same in each trial.
> What may the origin of the difference in the number of non-H-H potential
> bond pairs.

Only if the input structures are _exactly_ the same. In many cases, even a
simple rigid-body transformation in a PDB file (or another format with very
low coordinate precision), the computed distances may change simply
because the coordinates are held in such low precision that distances can't
be computed more precisely.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 06 2014 - 14:00:03 PST
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