Re: [AMBER] ptraj hbond output format

From: André C. Stiel <andre.stiel.tuebingen.mpg.de>
Date: Sun, 08 Dec 2013 12:39:54 +0100

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
>>
>
>


-- 
Dr. André C. Stiel
Researchgroup Protein Design
Max Planck Institute for Developmental Biology
Spemannstr. 35 72076 Tübingen, Germany
+49 7071 601 - 365
andre.stiel.tuebingen.mpg.de
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Received on Sun Dec 08 2013 - 04:00:02 PST
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