Re: [AMBER] ptraj hbond output format

From: Jan-Philip Gehrcke <jgehrcke.googlemail.com>
Date: Sun, 08 Dec 2013 16:26:40 +0100

He is probably using the latest, i.e. cpptraj from AmberTools 13
including all patches (http://ambermd.org/bugfixesat.html). From my
point of view cpptraj is one of the fastest evolving program within
AmberTools and it's really worth following the updates...


Cheers,

Jan-Philip



On 08.12.2013 12:39, "André C. Stiel" wrote:
> Hi Dan, thanks a lot for your help ...
> Which version of cpptraj are u using?
> Because with the Amber12 version it does not understand the keywords:
> "write", "run", "printatomnum" or "series", e.g.:
> "Warning: [hbond] Not all arguments handled: [ series ]"
> Maybe I do something wrong?
> The series command however works in cptraj from Amber11.
> Full output of your suggestion:
> CPPTRAJ: Trajectory Analysis. V12.4
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
> > [trajin prorun_reimaged.mdcrd 1 5]
> [prorun_reimaged.mdcrd] contains 17432 frames.
> > [hbond HB out hbond.dat .N,C,H,O series avgout hbavg.dat printatomnum]
> > [run]
> Warning: Unknown Command run.
> > [write solutehb.dat HB[solutehb]]
> Warning: Unknown Command write.
> >
> INPUT TRAJECTORIES:
> [prorun_reimaged.mdcrd] is an AMBER trajectory, Parm 0 (with box
> info) (reading 5 of 17432)
> Coordinate processing will occur on 5 frames.
>
> PARAMETER FILES:
> 0: xyz_wat.prmtop, 27597 atoms, 7795 res, non-ortho. box, 7455 mol,
> 7396 solvent mol, 5 frames
>
> REFERENCE COORDS:
> No reference coordinates.
> No frames defined.
>
> OUTPUT TRAJECTORIES:
> No files.
>
> ACTIONS: Initializing 1 actions:
> 0: [hbond HB out hbond.dat .N,C,H,O series avgout hbavg.dat printatomnum]
> HBOND: Searching for Hbond donors/acceptors in region specified by
> .N,C,H,O
> Distance cutoff = 3.000, Angle Cutoff = 135.000
> Dumping # Hbond v time results to hbond.dat
> Dumping Hbond avgs to hbavg.dat
> Warning: [hbond] Not all arguments handled: [ series printatomnum ]
>
>
> Thanks a lot !!!
>
>
>
>> Hi,
>>
>> Cpptraj will write out total # of solute-solute hbonds (and optionally
>> solute-solvent hbonds and # bridging waters) to the file specified by 'out
>> <filename>'. If you want raw time series data, you can specify 'series',
>> which will lead to a data set being created for each hbond seen over the
>> course of the input trajectory; solute-solute hbonds have aspect [solutehb]
>> and solute-solvent hbonds have aspect [solventhb]. These data sets have 1
>> for hbond present and 0 otherwise. You can write them all to a file once
>> trajectory processing is done via the write command, for example:
>>
>> parm input.parm7
>> trajin input.nc
>> hbond HB out hbond.dat .N,C,H,O series avgout hbavg.dat printatomnum
>> run
>> write solutehb.dat HB[solutehb]
>>
>> This runs the Hbond command looking for hydrogen bonds in the given mask
>> selection (in this case just some protein backbone atoms). This will
>> generate 3 files: hbond.dat will have the total # solute-solute hbonds,
>> hbavg.dat will have the average occupancies etc for each hbond seen, and
>> solutehb.dat will have the raw occupancy vs time for each hbond (in
>> columns). The 'printatomnum' command will print the atom number for each
>> hbond in hbavg.dat. You can obtain grace or gnuplot style output for
>> hbond.dat/solutehb.dat by changing the extension to .agr/.gnu respectively.
>>
>> Hope this helps,
>>
>> -Dan
>>
>> PS - You can also run lifetime analysis on the data generated by adding
>> something like this after the 'run' command:
>>
>> runanalysis lifetime HB[solutehb] out lifehb.dat
>>
>>
>>
>> On Fri, Dec 6, 2013 at 6:39 AM, Andre C. Stiel <andre.stiel.tuebingen.mpg.de
>>> wrote:
>>> hi all,
>>>
>>> is there a way to change the output format of the hbond command in
>>> ptraj....
>>> I mean the graphical .**x*@@ style is quite nice, but for something
>>> sheer occupancy number to plot against the simulation time would be nicer.
>>> Is there a way to accomplish that?
>>>
>>> Cheers
>>>
>>> André
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
>


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Received on Sun Dec 08 2013 - 07:30:02 PST
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