Hi Hadeer
It's donormask and acceptormask, in one word, not with spaces.
Second, you only need to specify the heavy atom not the hydrogen bound to
it, or at least I never did it
I will probably specify in the trajin line the keyword 'binpos' that
corresponds to the type of trajectory you are using, because I think that
ptraj understand by default the traditional mdcrd files.
the final line I do not know if it's OK, because I never used ptraj for the
hbond analysis, I use cpptraj, the new utility that eventually will
substitute ptraj. In my case I used something like this:
/panfs/panasas01/chem/chxrl/amber_gpu/amber12/bin/cpptraj $TOP << EOF
trajin $NC netcdf 1 5000 10
autoimage
hbond acceptormask :240 solventdonor :WAT dist 3.5 out HB_ac_KQ.dat avgout
HB_ac_KQ_avg.dat
hbond donormask :240 solventacceptor :WAT dist 3.5 out HB_do_KQ.dat avgout
HB_do_KQ_avg.dat
EOF
Hope this is useful to you.
Have a nice weekend
2015-10-17 16:06 GMT+02:00 Hadeer ELHabashy <hadeer.elhabashi.gmail.com>:
> Dear sir
>
> Kindly which one of the following commands are functioning correctly with
> cpptraj of Ambertools 15 ?
>
> file.trajin
>
> trajin md.binpos
> donor mask :1.N
> acceptor mask :6.OXT :1.H1
> hbond print .05 series hbt
>
> and every time i got such errors
>
> Error: 'donor' is deprecated.
> Hydrogen bond acceptors and donors are defined within the 'hbond' action.
> Error: Unrecognized character in expression: :
> 'donor mask :1.N': Invalid command or expression.
> 'donor mask ALA N': Invalid command or expression.
> 'donormask:1.N': Invalid command or expression.
>
> Regards
> Hadeer
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>
--
Dr. Emilio Lence Quintana
Organic Chemistry Department-CIQUS
University of Santiago de Compostela
15782 Santiago de Compostela, Spain
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Received on Sat Oct 17 2015 - 07:30:04 PDT
