Actually I am now running this
trajin md.crd
hbond out N_H1_OXT.out donormask :1.N donorhmask :1.H1 acceptormask :6.OXT
series hbt
hbond out N_H2_OXT.out donormask :1.N donorhmask :1.H2 acceptormask :6.OXT
series hbt
hbond out N_H3_OXT.out donormask :1.N donorhmask :1.H3 acceptormask :6.OXT
series hbt
hbond out N_H1_OXT.out donormask :1.N donorhmask :1.H1 acceptormask :6.O
series hbt
hbond out N_H2_OXT.out donormask :1.N donorhmask :1.H2 acceptormask :6.O
series hbt
hbond out N_H3_OXT.out donormask :1.N donorhmask :1.H3 acceptormask :6.O
series hbt
On Sat, Oct 17, 2015 at 5:20 PM, 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>
> 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 - 08:30:09 PDT
