You're trying to name data in each command 'hbt'. Replace 'hbt' with
something else in the second command.
-Dan
On Saturday, October 17, 2015, Hadeer ELHabashy <hadeer.elhabashi.gmail.com>
wrote:
> 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
> <javascript:;>>
> 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 <javascript:;>> 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
> <javascript:;>>
> > > wrote:
> > >
> > > > On Sat, Oct 17, 2015 at 11:05 AM, Hadeer ELHabashy <
> > > > hadeer.elhabashi.gmail.com <javascript:;>> 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 <javascript:;>
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org <javascript:;>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > 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 Sat Oct 17 2015 - 08:30:10 PDT
