[AMBER] Re :checkoverlap

From: John S <s.john634.gmail.com>
Date: Wed, 17 Mar 2010 23:45:37 -0400

Dear Amber Users ,

I used Amber tools (ptraj) ,checkoverlap to get the number of residues
clustering at a particular frame of my trajectory file (i.e within a
distance of 1 Angstorm ) .No output file was generated .

For example if I have 5 residues

trajin trajectory.x 1000 1000
checkoverlap :1,2,3,4,5 min 1.0 around :1,2,3,4,5

What is the format of output file for this tool and where should I specify
it .
I would also like to know whether this is the suitable tool to know the
clustering of residues .
Your suggestion are highly appreciated .

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Received on Wed Mar 17 2010 - 21:00:03 PDT
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