How to "solve" ligand (STU) in 1Q3D protein to use with PyRx

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How to "solve" ligand (STU) in 1Q3D protein to use with PyRx

Postby bsantoso » Sat Jul 11, 2015 9:57 am

Hi Sargis, congrats for your book chapter.

I use PyRx 0.9.2 for mac. I converted ligand STU (attached, from PDB code: 1Q3D) to pdbqt using PyRx successfully but when I wanted to use it for vina, I got "error branch" for the molecule. How to solve this problem?

Thanks

bsantoso
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1Q3D_Alig.sdf
raw molecule from protein for chain A
(4.61 KiB) Downloaded 123 times
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Re: How to "solve" ligand (STU) in 1Q3D protein to use with

Postby bsantoso » Sat Jul 11, 2015 10:35 am

These are the error message and converted file (pdbqt). Thanks
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1Q3D_STU_A_451.pdbqt
converted file
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error_stu.jpg
error message
error_stu.jpg (193.12 KiB) Viewed 5543 times
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Re: How to "solve" ligand (STU) in 1Q3D protein to use with

Postby sargis » Sat Jul 11, 2015 8:31 pm

Hi Broto and thank you for the message.

I've searched for "has not been found in this branch" and found that this has been fixed in the latest version of ADT. I plan to update ADT included with PyRx in the next release of PyRx to fix this. In the meantime, please used attached pdqt file instead. I've used PyRx's Open Babel widget to convert sdf to pdb and then used latest version of ADT to make attached pdbqt file.

Thank you for using PyRx!
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1Q3D_Alig.pdbqt
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Re: How to "solve" ligand (STU) in 1Q3D protein to use with

Postby bsantoso » Sat Jul 11, 2015 9:49 pm

Thank you Sargis, hopely the update will come soon.
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Re: How to "solve" ligand (STU) in 1Q3D protein to use with

Postby sargis » Sat Nov 28, 2015 7:43 pm

bsantoso wrote:Thank you Sargis, hopely the update will come soon.

You are very welcome. Please update your version of PyRx using Help->Check for Updates... option. You'll also need to download latest AutoDockTools from http://mgldev.scripps.edu/cgi-bin/viewv ... /?view=tar

Extract this at the following location so that it will overwrite AutoDockTools that is already there:
/Library/PyRx/0.9.2/Python.framework/Versions/2.6/lib/python2.6/site-packages/

Close and start PyRx for it to load latest version of AutoDockTools. These changes are supposed to fix "Atom xx has not been found in this branch" error and PyRx would also skip ligands that are giving other errors.

Thank you!
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Re: How to "solve" ligand (STU) in 1Q3D protein to use with

Postby bsantoso » Sun Nov 29, 2015 12:24 am

Thank you Sargis,

I have trouble when updating, is it correct, firstly, I update the pyrx then replace with your file?
I have try partial or all content of folder AutoDockTools but got error and pyrx cannot open
here the error for partial
Code: Select all
Traceback (most recent call last):
  File "/Library/PyRx/0.9.2/runPyRx.py", line 71, in <module>
    startPyRx()
  File "/Library/PyRx/0.9.2/runPyRx.py", line 39, in startPyRx
    frame = MainFrame(None, -1, size=(width, height-200))
  File "/Library/PyRx/0.9.2/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/wxMainFrame.py", line 151, in __init__
    self.autodockWiz = AutoDockWizard(self) #AutoDock controls
  File "/Library/PyRx/0.9.2/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/autodockWizard.py", line 122, in __init__
    from autodockPage import RunAutoDock
  File "/Library/PyRx/0.9.2/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/autodockPage.py", line 14, in <module>
    from traitedDockingParameters import TraitedDockingParameters, TraitedGeneticAlgorithmParameters, \
  File "/Library/PyRx/0.9.2/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/traitedDockingParameters.py", line 8, in <module>
    class TraitedDockingParameters( HasTraits ):
  File "/Library/PyRx/0.9.2/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/traitedDockingParameters.py", line 28, in TraitedDockingParameters
    tstep = Float(dpo['tstep']['value'][0])
TypeError: 'float' object is unsubscriptable

Problem starting PyRx. Please visit PyRx forum for a possible solution: http://mgl.scripps.edu/forum

and full folder
Code: Select all
Traceback (most recent call last):
  File "/Library/PyRx/0.9.2/runPyRx.py", line 71, in <module>
    startPyRx()
  File "/Library/PyRx/0.9.2/runPyRx.py", line 39, in startPyRx
    frame = MainFrame(None, -1, size=(width, height-200))
  File "/Library/PyRx/0.9.2/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/wxMainFrame.py", line 130, in __init__
    import preferences
  File "/Library/PyRx/0.9.2/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/preferences.py", line 20, in <module>
    from vsModel import autodockPreferencesPage, ligandPreparationPage, autodockRemotePreferencesPage
  File "/Library/PyRx/0.9.2/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/vsModel.py", line 7, in <module>
    from AutoDockTools.MoleculePreparation import AD4LigandPreparation, AD4ReceptorPreparation, AD4FlexibleReceptorPreparation
ImportError: No module named AutoDockTools.MoleculePreparation

Problem starting PyRx. Please visit PyRx forum for a possible solution: http://mgl.scripps.edu/forum


Need your assisstance, thanks
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Re: How to "solve" ligand (STU) in 1Q3D protein to use with

Postby sargis » Sun Nov 29, 2015 12:50 am

You are welcome Broto and sorry about this. Please download http://pyrx.sourceforge.net/updates/pyrx_093.tar.gz and extract PyRx folder at the following location so that it will overwrite PyRx folder that is already there:
/Library/PyRx/0.9.2/Python.framework/Versions/2.6/lib/python2.6/site-packages/

If you see updates folder in /Users/bsantoso/Desktop/PHP/../../workspace, remove that folder. Also run the following from a command line:
sudo chmod -R 777 /Library/PyRx/0.9.2/Python.framework/Versions/2.6/lib/python2.6/site-packages/

Please let me know if this fixed these errors. Thank you.
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Re: How to "solve" ligand (STU) in 1Q3D protein to use with

Postby bsantoso » Sun Nov 29, 2015 1:28 am

Thanks Sargis, it is working like charm now.

Is it correct, that you remove maximize button in Vina Search Space? And I see a different appearance for parameters button and dropdown menu above Vina Search Space, too. :)

Thank you again, Sargis
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Re: How to "solve" ligand (STU) in 1Q3D protein to use with

Postby sargis » Sun Nov 29, 2015 2:02 am

bsantoso wrote:Thanks Sargis, it is working like charm now.

Great, glad it's working. I'll be making a new 0.9.3 release soon that would include what you have downloaded, plus maybe some additional last minute bug fixes. The Changelog for the upcoming 0.9.3 release is at https://sourceforge.net/p/pyrx/wiki/Changelog/

You can apply these changes to Windows and Linux versions as well by unpacking PyRx and AutoDockTools at these locations instead:
  • Windows - C:\Program Files (x86)\PyRx\$Version\Lib\site-packages
  • Linux - /usr/local/PyRx-$Version/lib/python2.6/site-packages
bsantoso wrote:Is it correct, that you remove maximize button in Vina Search Space? And I see a different appearance for parameters button and dropdown menu above Vina Search Space, too. :)

This is correct, I removed maximize button in Vina Search Space. The reason for this is that I've added inverse virtual screening option so that now you can dock multiple ligands against multiple receptors. Since it would be time consuming to go and click on maximize button when you work with multiple receptors, now PyRx sets the initial grid box maximized to include all receptor atoms. The dropdown menu is there so that you can select different receptors and change grid space as needed for each receptors.

Hope this makes sense and I appreciate your feedback.
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Re: How to "solve" ligand (STU) in 1Q3D protein to use with

Postby bsantoso » Sun Nov 29, 2015 5:45 am

Ok, Sargis. It is superb feature. Thanks
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