Thank you.
On Nov 27, 2017 6:27 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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>
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Received on Mon Nov 27 2017 - 09:00:03 PST
