AMBER Archive (2006)

Subject: AMBER:Checkoverlap query

From: sangeeta_at_bioinfo.ernet.in
Date: Mon Jun 26 2006 - 07:12:56 CDT

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

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Thanks for any suggestions.

Sangeeta Sawant
Bioinformatics Centre
University of Pune
India

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