[AMBER] cpptraj hbond: query on output

From: George Tzotzos <gtzotzos.me.com>
Date: Thu, 09 Oct 2014 17:33:25 -0300

Iím trying to work out h-bonds and bridged h-bonds between a ligand and receptor residues ONLY.

I used the following script

hbond REC-LIG donormask :1-125 acceptormask :126 out Nhbond.agr avgout REC-LIG.dat bridgeout Bridge.dat solventdonor :WAT solventacceptor :WAT.O

When I draw (xmgrace) the output Nhbond.agr shows three series REC-LIG[UU], REC-LIG[UV] and REC-LIG[Bridge].

The output shows the maximum of per frame interactions to be 2 in the case of REC-LIG[UU] series and 12 in the case of REC-LIG[UV]. The difference between the two datasets is not quite clear to me. Any explanation and/or improvement in the above script would be most helpful.

Iím attaching a graphical output for easy reference


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Received on Thu Oct 09 2014 - 14:00:02 PDT
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