Thank's
> Date: Mon, 22 Aug 2011 11:47:35 -0400
> From: daniel.r.roe.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] hbond atom mask in cpptraj
>
> Hi,
>
> The "hbond" command in cpptraj is at the moment a much simpler version
> than the one found in ptraj and is designed to quickly provide
> information on hydrogen bonds in the region specified by "mask".
> Unlike ptraj, cpptraj does not use "donor" or "acceptor" commands to
> define hydrogen bonds; instead, it searches the mask region for all
> potential donors and acceptors (currently following the simplistic
> criterion that "hydrogen bonds are FON", i.e. only hydrogens bound to
> F, O, and N are considered). If you want to be able to specify which
> atoms to study for hydrogen bonding you currently need to use ptraj.
>
> So, to answer your original questions first:
> > 1/ hbond between resid1-resid1
> hbond out NHB-residue1.dat :1 avgout AvgHB-residue1.dat
>
> > 2/ hbond between resid1-resid2
> hbond out NHB-r1r2.dat :1,2 avgout AvgHB-r1r2.dat
>
> Unfortuntaely in this case there is no way in cpptraj to not look at
> hbonds between res1-res1 and res2-res2 since the search for donors and
> acceptors is automatic.
>
> > 2/ hbond between resid1-water
> Unfortunately not yet implemented in cpptraj (since each water
> molecule will currently be considered a separate residue); handling of
> solvent Hbonds will be present in the next release of cpptraj. For now
> you should just use ptraj for studying solvent-solute hbonds.
>
> -Dan
>
>
> On Sat, Aug 20, 2011 at 7:16 PM, mirage . <m.o.m.live.fr> wrote:
> >
> >
> >
> >> From: m.o.m.live.fr
> >> To: amber.ambermd.org
> >> Date: Sat, 20 Aug 2011 17:50:12 +0000
> >> Subject: Re: [AMBER] hbond atom mask in cpptraj
> >>
> >> >
> >> >
> >> > Hi Amber users,
> >> >
> >> > I want to count hbond with cpptaraj.
> >
> >
> >> > 1/ hbond between resid1-resid1
> >
> > i do this by "donnor :1" (= or "acceptor :1")
> >
> >> > 2/ hbond between resid1-resid2
> >
> > if i do" donnor :1,:2" or "acceptor :1,:2" in the result i found: (hbond resid1-resid1)+ (hbond resid2-resid2)+ (hbond resid1-resid2)
> > How to exclude the inter-hbond (hbond resid1-resid1)+ (hbond resid2-resid2)
> >
> > I want to count just the intermolucular hbond between residu
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Received on Mon Aug 22 2011 - 09:30:04 PDT
