Hi again.
Rereading your mail I see that you use cpptraj. The problem apart of what I
said before is that you have to use acceptormak or donormask in the same
line that starts with hbond command. see the example that I put in my
previous answer.
Just for clarity $TOP and $NC are variables that I use in my script that
corresponds to the topology file and the trajectory file.
Have a nice weekend
2015-10-17 16:23 GMT+02:00 Emilio Lence <guitarro.de.meixente.gmail.com>:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Dr. Emilio Lence Quintana
> Organic Chemistry Department-CIQUS
> University of Santiago de Compostela
> 15782 Santiago de Compostela, Spain
>
--
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 - 08:00:06 PDT
