Take away the masks as well their corresponding keywords. If you want you
can use a single mask, :1-126, but the automatic detection should be enough
unless you have more than the two solute molecules.
-Dan
On Thursday, October 9, 2014, George Tzotzos <gtzotzos.me.com> wrote:
> Thank you Dan
>
> I’d be grateful of some additional clarifications.
>
> If I modify the script according to your suggestion (see below) - which I
> may have misunderstood -
>
> hbond H1 :1-125 :126 nointramol out Nhbond2.agr avgout avg2.dat
> bridgeout Bridge2.dat solventdonor :WAT solventacceptor :WAT.O
>
> I get a warning: Warning: [hbond] Not all arguments handled: [ :126 ]
>
> and as a consequence no h-bonding interactions of the ligand. Please note
> :126 is the ligand.
>
> One additional clarification concerning the definition for [UU]
> (solute-solute bonds). The solute in my case is the receptor-ligand
> complex. I guess [UU] then refers to receptor-ligand h-bonds. Am I wrong?
>
> Thanks once again for your help
>
> George
>
>
> On 9Oct, 2014, at 7:24 PM, Daniel Roe <daniel.r.roe.gmail.com
> <javascript:;>> wrote:
>
> > Hi,
> >
> > On Thu, Oct 9, 2014 at 2:33 PM, George Tzotzos <gtzotzos.me.com
> <javascript:;>> wrote:
> >> I’m trying to work out h-bonds and bridged h-bonds between a ligand and
> receptor residues ONLY.
> >
> > If you just want ligand-receptor hbonds You will want to add the
> > 'nointramol' keyword to your 'hbond' command so that intra-molecular
> > hydrogen bonds are ignored. If you can probably get rid of your
> > 'donormask' and 'acceptormask' keywords and let cpptraj search for
> > donors and acceptors. What these keywords are doing right now is
> > looking for hbond donors in your receptor only and hbond acceptors in
> > your ligand only - you really want both acceptors and donors for each.
> >
> >> I used the following script
> >>
> >> hbond REC-LIG donormask :1-125 acceptormask :126 out Nhbond.agr avgout
> REC-LIG.dat bridgeout Bridge.dat solventdonor :WAT solventacceptor :WAT.O
> >>
> >> When I draw (xmgrace) the output Nhbond.agr shows three series
> REC-LIG[UU], REC-LIG[UV] and REC-LIG[Bridge].
> >>
> >> The output shows the maximum of per frame interactions to be 2 in the
> case of REC-LIG[UU] series and 12 in the case of REC-LIG[UV]. The
> difference between the two datasets is not quite clear to me. Any
> explanation and/or improvement in the above script would be most helpful.
> >
> > These are described in the Amber 14 manual in the cpptraj hbond
> > command (28.10.24):
> >
> > [UU] Number of solute-solute hydrogen bonds.
> > [UV] Number of solute-solvent hydrogen bonds.
> > [Bridge] Number of bridging solvent molecules.
> >
> > Hope this helps,
> >
> > -Dan
> >
> >>
> >> I’m attaching a graphical output for easy reference
> >>
> >> Regards
> >>
> >> George
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org <javascript:;>
> >> 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 <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> 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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Received on Thu Oct 09 2014 - 18:30:02 PDT
