AMBER:Checkoverlap query

From: <>
Date: Mon, 26 Jun 2006 17:42:56 +0530 (IST)

I would like to find the structures from my MD trajectory which have
bad contacts (short contacts). The CHECKOVERLAP output lists several atom
pairs that are bonded directly. If I wish to get a list of only non-bonded
atoms closer than a cut-off, is there any way?
While searching the AMBER mail reflector archive I found the following
similar query by Gustavo. However, I could not find any reply in the
same thread:
From: Gustavo Pierdominici Sottile <> Date: Thu Jun 02
2005 -18:45:19 BST contacts.
Dear Amber users:
      I am using ptraj and want to see how and which
      pair of atoms are less than 2.5 A.
      When using checkoverlap in ptraj with min 2.5, it appears a list of
      atoms pairs that are less than 2.5. But those pairs are bonded
      atoms. I would like to find pairs of atoms that are close but
      If someone knows, please, let me know.
                        Thanking in advance

Thanks for any suggestions.

Sangeeta Sawant
Bioinformatics Centre
University of Pune

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Received on Tue Jun 27 2006 - 09:53:47 PDT
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