[AMBER] HBOND_water mediated

From: Lara rajam <lara.4884.gmail.com>
Date: Mon, 14 Dec 2015 10:16:58 -0500

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


#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
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