problem with minimization movie

Asked by Francisco García on 2013-10-27

Hi,

I am using the procedure to visualize all conformations taken by the ligand during minimizations.

I generate docking.clust file where I can see translations and rotations, is the follow:

      Trans Rot Ener RmsdCA_ref Rank Weight
== 1 1 -57.4844249 0.937420362399 1 1

I use startligand.py to generate the ligand_X_Y.red file,

startligand.py ligand.red 1 1

But I get the following error when executing the previous script:

fran@fran:~/soft/ptools-develop/PyAttract$ startligand.py ligand.red 1 1
Translation file: translation.dat
Rotation file: rotation.dat
Target translation number: 1
Target rotation number: 1
Traceback (most recent call last):
  File "/home/fran/soft/ptools-develop/PyAttract/startligand.py", line 103, in <module>
    target_trans_val=trans.GetCoords(target_trans_nb)
AttributeError: '_ptools.Rigidbody' object has no attribute 'GetCoords'

Regards

Question information

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Status:
Answered
For:
PTools Edit question
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Last query:
2013-10-28
Last reply:
2013-11-14

Hi Francisco,

Thank you for the report.

This was a bug. I fixed the "startligand.py" script (and also applytraj.py). I think you should now be able to generate a pdb containing a trajectory.

Best regards,
Adrien

Hi Adrien,

Thanks for the fix.

I found another bug when running the irsmd.py script, is the follow:

fran@fran:~/soft/ptools-develop/PyAttract$ irmsd.py receptor.red ligand.red ligand_1.red
Traceback (most recent call last):
  File "/home/fran/soft/ptools-develop/PyAttract/irmsd.py", line 94, in <module>
    main()
  File "/home/fran/soft/ptools-develop/PyAttract/irmsd.py", line 90, in main
    IRMSD=irmsd(rec,lig,lig2,None,True)
  File "/home/fran/soft/ptools-develop/PyAttract/irmsd.py", line 39, in irmsd
    pairlist = AttractPairList(receptor, ligref, cutoff) #pairlist created on protein backbone + side-chains
  File "pairlist.pyx", line 76, in _ptools.AttractPairList.__cinit__ (_ptools.cpp:9527)
    raise TypeError("arguments error in AttractPairList.__cinit__()")
TypeError: arguments error in AttractPairList.__cinit__()

Regards.

Launchpad Janitor (janitor) said : #3

This question was expired because it remained in the 'Open' state without activity for the last 15 days.

I fixed the irmsd.py script in the github repository.

answered

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