I’m interested to find H-bonds between residue 126 (ligand) other protein residues as well as solvent (HOH).
I’m 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
go
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.
Regards
George
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Received on Wed Sep 10 2014 - 13:30:03 PDT
