AMBER:Checkoverlap query

From: <sangeeta.bioinfo.ernet.in>
Date: Mon, 26 Jun 2006 17:42:56 +0530 (IST)

Hi,
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 <gsottile.unq.edu.ar> 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
      non-bonded
      If someone knows, please, let me know.
                        Thanking in advance
                        Gustavo

---------------------------------------------------
Thanks for any suggestions.

Sangeeta Sawant
Bioinformatics Centre
University of Pune
India


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