Hai ! Dan !
Thank you so much I will try this !
let me know in future if you implement this
thank you once again
On Tue, Dec 15, 2015 at 12:01 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> If I understand what you want, which I think is to specifically get
> Protein-Water-Ligand hydrogen bonds, I don't believe there is
> currently a way to do this. Probably the best you could do would be to
> use the closest command to retain a small shell of water around your
> bridging residues of interest and then do hbond analysis on that. For
> example, if you have this kind of bridging output:
>
> #Bridging Solute Residues:
> Bridge Res 10:THR 11:TRP , 5 frames.
>
> You could do something like
> closest 10 :10,11 first
> hbond Res10-11 distance 3.5 angle 12 :10,11 ...
>
> etc
>
> It might be a useful thing in the cuture to add some kind of time
> series data to the bridging output. I'll look into that.
>
> -Dan
>
>
> On Mon, Dec 14, 2015 at 8:16 AM, Lara rajam <lara.4884.gmail.com> wrote:
> > 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 !
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Dec 17 2015 - 07:00:04 PST
