finally I ran this successfully, but I got all Zeros and that is strange!
I ran with NVT with Langevin thermostat and all interaction calculated
hbond out N_H1_OXT.out donormask :1.N donorhmask :1.H1 acceptormask :6.OXT
dist 3.5 series h1
hbond out N_H2_OXT.out donormask :1.N donorhmask :1.H2 acceptormask :6.OXT
dist 3.5 series h2
hbond out N_H3_OXT.out donormask :1.N donorhmask :1.H3 acceptormask :6.OXT
dist 3.5 series h3
what if I want to get the life time of the bond ?
should just write life time in the command ?!
On Sat, Oct 17, 2015 at 5:22 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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>
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Received on Sat Oct 17 2015 - 09:30:04 PDT
