[AMBER] ptaj: contacts

From: George Tzotzos <gtzotzos.me.com>
Date: Fri, 03 Jun 2011 17:31:53 +0200

Hi everybody,

I'm following the instructions of AmberTools manual to find the contacts between a bound ligand and a receptor protein of 124 residues. The input trajectory file has 200 sets

I'm using the following script for the purpose:

trajin prod_6ns.mdcrd
strip :WAT
strip :Na+
contacts first byresidue out contacts.out time 1 distance 7.0 :125

I obtain two output files as expected (contacts.out and contacts.out.native) of the form:

#time residue 124
      1.00 161818
      2.00 159818

What do the 6-digit numbers under residue represent? Certainly NOT residues.

Any help on how to improve the script would be much appreciated.



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Received on Fri Jun 03 2011 - 09:00:03 PDT
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