Actually when I visualize the system with VMD , I can visualize many
hydrogen bondings
but AMBER did not detected it
On Sat, Oct 17, 2015 at 6:09 PM, Hadeer ELHabashy <
hadeer.elhabashi.gmail.com> wrote:
> 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 - 10:00:03 PDT
