Reading 'mol.top' as Amber Topology
INPUT: Reading Input from STDIN
[trajin 2y3j_pc_md.crd]
Reading '2y3j_pc_md.crd' as Amber Trajectory
[hbond out N_H1_OXT.out donormask :1.N donorhmask :1.H1 acceptormask
:6.OXT series hbt]
HBOND: Donor mask is :1.N, Acceptor mask is :6.OXT
Separate donor H mask is :1.H1
Distance cutoff = 3.000, Angle Cutoff = 135.000
Writing # Hbond v time results to N_H1_OXT.out
Time series data for each hbond will be saved for analysis.
[hbond out N_H2_OXT.out donormask :1.N donorhmask :1.H2 acceptormask
:6.OXT series hbt]
Warning: DataSet 'hbt[UU]' already present.
On Sat, Oct 17, 2015 at 5:16 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> What is the whole output? I think cpptraj usually prints hints about what
> error it encountered.
>
> On Sat, Oct 17, 2015 at 11:14 AM, Hadeer ELHabashy <
> hadeer.elhabashi.gmail.com> wrote:
>
> > :)))
> >
> > trajin md.binpos
> > hbond out N_H1_OXT.out donormask :1.N donorhmask :1.H1 acceptormask
> > :6.OXT
> > series hbt
> >
> > yes, I got an error message
> > " Error: Could not initialize action [hbond]
> > 1 errors encountered reading input."
> >
> >
> >
> > On Sat, Oct 17, 2015 at 5:09 PM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> > > On Sat, Oct 17, 2015 at 11:05 AM, Hadeer ELHabashy <
> > > hadeer.elhabashi.gmail.com> wrote:
> > >
> > > > Dear Dr. Danial
> > > >
> > > > Thanks for help
> > > > I have checked cpptraj 'hbond', section 29.9.25. upon your
> > recommendation
> > > > and I came up with this lines for cpptraj
> > > >
> > > > trajin 2y3j_pc_md.crd
> > > > hbond out N_H1_OXT.out donormask :1.N donorhmask:1.H1 acceptormask
> > > :6.OXT
> > > > series hbt
> > > >
> > >
> > > You need a space between donorhask and :
> > >
> > >
> > > > what do you think may be wrong or missing in the second line ?!
> > > >
> > >
> > > Did you get an error when you tried to use it? If so, what was the
> > error
> > > message? I prefer video games to guessing games myself :).
> > >
> > > HTH,
> > > Jason
> > >
> > > --
> > > Jason M. Swails
> > > BioMaPS,
> > > Rutgers University
> > > Postdoctoral Researcher
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Oct 17 2015 - 08:30:08 PDT
