[AMBER] Hydrogen bond analysis Through CPPTRAJ

From: Rana Rehan Khalid <rrkhalid.umich.edu>
Date: Sun, 26 Nov 2017 19:03:15 +0500

Dear Amber Users

I want to know. How we do the hydrogen bond analysis for Heme , NO like
hetroatoms. I ran the cpptraj command but it shows the hydrogen bond for
only residues not for the heme or NO. which is the part of my system.
Kindly guide If any tutorial is explained it.

script i used is this

# Hydrogen bond analysis with cpptraj
# Load topology and trajectory
parm noH_solv.prmtop
trajin noH_5.mdcrd
# All solute-solute and solute-solvent hydrogen bonds + water bridges.
hbond All out All.hbvtime.dat solventdonor :WAT solventacceptor :WAT.O \
  avgout All.UU.avg.dat solvout All.UV.avg.dat bridgeout All.bridge.avg.dat
# Backbone hydrogen bonds only. Save time series data.
hbond Backbone :1-189.C,O,N,H avgout BB.avg.dat series uuseries bbhbond.gnu
# Create file containing only number of solute-solute and solute-solvent
# hydrogen bonds, and number of solute-solvent-solute bridges.
create nhbvtime.agr All[UU] Backbone[UU] All[UV] All[Bridge]
# Calculate RMSD to first frame.
rms BBrmsd :1-189.C,CA,N out BBrmsd.agr
# Run to actually find hydrogen bonds and generate data.
# Perform lifetime analysis on backbone hydrogen bonds
lifetime Backbone[solutehb] out backbone.lifetime.dat
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Received on Sun Nov 26 2017 - 06:30:02 PST
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