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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 15 2015 - 09:30:05 PST
