[AMBER] hbond lifetime

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 10 Sep 2014 17:13:13 -0300

Iím interested to find H-bonds between residue 126 (ligand) other protein residues as well as solvent (HOH).

Iím using the following script to run cpptraj bond

trajin prod_0-20ns.nc
hbond H1 series acceptormask :126&.N*,O* donormask :1-125&.N*,O*
hbond out hb.dat dist 3.0 avgout avg.dat \
bridgeout bridgeout.dat solventdonor :WAT solventacceptor :WAT&.O
runanalysis lifetime H1 [hb.dat] out life.dat

The script produces: avg.dat; bridgeout.dat and hb.dat. If fails to produce life.dat due to Error: lifetime: No datasets selected.

Any help in improving the script will be much appreciated.



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Received on Wed Sep 10 2014 - 13:30:03 PDT
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