Hi,
Do you expect there to be any hydrogen bonds? Maybe the default
distance/angle criteria are more restrictive than you want? FYI you
can check specifically what donors/acceptors are defined by specifying
'debug actions 1' prior to the 'hbond' command.
-Dan
On Sun, Nov 26, 2017 at 9:03 AM, Rana Rehan Khalid <rrkhalid.umich.edu> wrote:
> 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.
>
> Regards
> 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.
> run
> # Perform lifetime analysis on backbone hydrogen bonds
> lifetime Backbone[solutehb] out backbone.lifetime.dat
> runanalysis
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Nov 27 2017 - 08:30:04 PST
