Dear Amber !
I am trying to calculate the HBOND using cpptraj.
I was able to do for the protein ligand complex without water.
Now, I am trying to calculate the number of solvent interactions between
the ligand and the protein. I was able to do for the whole water
interaction as below
trajin 50.mdcrd
hbond MyHB distance 3.5 angle 120 :1-75 out xnhb.dat avgout xavghb.dat
nointramol solventacceptor :WAT solventdonor :WAT solvout solvent_avg.dat
bridgeout bridge.dat series
run
#writedata solutehb.dat MyHB[solutehb]
writedata solventhb.dat MyHB[solventhb]
#lifetime MyHB[solutehb] out solute.lifetime.dat
lifetime MyHB[solventhb] out solvent.lifetime.dat
run analysis
here , 1-75 including the ligand , 1-73 is protein and 74-75 is ligand ,
how to make it more specific , like only protein water ligand hydrogen bond
and their number.
some insight will help to understand better
thank you !
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Received on Mon Dec 14 2015 - 07:30:03 PST
