Error while conversion of multiple ligands into pdbqt

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Error while conversion of multiple ligands into pdbqt

Postby ajeetmdl23 » Sun Nov 15, 2015 7:08 pm

Hi Sargis,
I am trying to prepare ligands from .sdf file downloaded (Natural Products Set II: https://wiki.nci.nih.gov/display/NCIDTP ... pound+Sets) for the virtual screening using PyRx 0.9 on OSX 10.11.1
After adding the .sdf file as input using 'control' tab 'OpenBabel', I do energy minimization to all ligands and then I convert all the ligands into pdbqt formate. But, unfortunately I keep getting this (attached file) error and I am not able to figure out how to fix this problem. Could you please guide me to fix this problem. I wonder if there is a standard way of pre-processing the .sdf file with multiple ligands which one should go through before any enery minimization and pdbqt conversion.
Note: It's not the only .sdf file that gives me such error, there are other files too. Please see the attached error log file.
Thanks,
Ajeet
NIH/NIDCR
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Nat2_error copy.log
Error log file
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Re: Error while conversion of multiple ligands into pdbqt

Postby sargis » Sun Nov 15, 2015 10:31 pm

Hi Ajeet,

Thank you for the message. I've download sdf for NCI Natural Products Set II from the link you sent and I see that, for instance, there is this compound there called Rifamycin sodium salt:
133100.png
133100.png (12.82 KiB) Viewed 4349 times

I don't know how sdf for NCI Natural Products Set II were made, but it's hard for OpenBabel to generate plausible 3D conformation starting with this 2D structure. For this molecule, you can download sdf of 3D Conformer from PubChem and use that instead - https://pubchem.ncbi.nlm.nih.gov/compou ... -Conformer

You can also get AutoDock "pdbqt" format files from ZINC - http://docking.org/node/263

Thank you for using PyRx!
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Re: Error while conversion of multiple ligands into pdbqt

Postby ajeetmdl23 » Tue Nov 17, 2015 6:44 am

Thanks ! Sargis, for your quick reply. I realized that in some of the other libraries e.g NCI_Diversity set-V also contain such erroneous ligand entries, I had to replace them one after other with a correct sdf info. So, Yes ! your reply really helped. Thanks again :D .
Ajeet
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Re: Error while conversion of multiple ligands into pdbqt

Postby sargis » Wed Nov 18, 2015 3:44 am

ajeetmdl23 wrote:Thanks ! Sargis, for your quick reply. I realized that in some of the other libraries e.g NCI_Diversity set-V also contain such erroneous ligand entries, I had to replace them one after other with a correct sdf info. So, Yes ! your reply really helped. Thanks again :D .
Ajeet

You are very welcome Ajeet. Very happy to see my reply really helped. Thank you much for using PyRx.
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Error while docking large ligands -library

Postby ajeetmdl23 » Fri Nov 20, 2015 12:34 pm

Hi Sargis,
I am back with the similar trouble (error) as I discussed before. This time, while docking of ligands (after energy minimization and .pdbqt conversion nicely) downloaded from ZINC (http://zinc.docking.org/catalogs/ibsnp) I get the following attached errors. After running more than half way smoothly and a long wait, encountering an error that leads to a full-stop to entire experiment is kind of frustrating...isn't :? :roll: . Instead, I think, it would have been nicer to have skipped to the next ligand after printing error log.
I wonder if there is any standard way to assure the compound-library file quality or validation that is compatible for PyRx to run. Any help is appreciated from Sargis/other forum-members.
Best regards,
Ajeet
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Re: Error while docking large ligands -library

Postby sargis » Sat Nov 21, 2015 10:14 pm

ajeetmdl23 wrote:Hi Sargis,
I am back with the similar trouble (error) as I discussed before. This time, while docking of ligands (after energy minimization and .pdbqt conversion nicely) downloaded from ZINC (http://zinc.docking.org/catalogs/ibsnp) I get the following attached errors. After running more than half way smoothly and a long wait, encountering an error that leads to a full-stop to entire experiment is kind of frustrating...isn't :? :roll: . Instead, I think, it would have been nicer to have skipped to the next ligand after printing error log.
I wonder if there is any standard way to assure the compound-library file quality or validation that is compatible for PyRx to run. Any help is appreciated from Sargis/other forum-members.
Best regards,
Ajeet

Hi Ajeet,

I would certainly be happy to help you with this. The link you send is currently down and I couldn't find attached errors. I fixed the problem of going to the next ligand for the next release, I think. If you can send a test case, I can try I would be happy to.

I don't know of any standard way to assure compound-library file quality or validation that is compatible for PyRx to run. Maybe other forum-members can chime in. It can be garbage in, garbage out, unless there is some sort of quality assurance in between. That's a good question though; I'll think about this more for the upcoming releases.

Best regards,
Sargis
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Re: Error while conversion of multiple ligands into pdbqt

Postby ajeetmdl23 » Mon Nov 23, 2015 2:44 pm

Thanks Sargis for the quick reply and considering the points mentioned.
Also, I might forgot to attach the error log file. Attached now. Sorry for that.
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Re: Error while conversion of multiple ligands into pdbqt

Postby sargis » Mon Nov 23, 2015 3:59 pm

ajeetmdl23 wrote:Thanks Sargis for the quick reply and considering the points mentioned.
Also, I might forgot to attach the error log file. Attached now. Sorry for that.

Thank you Ajeet. Please update your version of PyRx using Help->Check for Updates... option. This updated version is supposed to skip ligands that are giving errors. Please let me know if it doesn't.

To fix "Atom 23 has not been found in this branch" error, please download latest AutoDockTools from http://mgldev.scripps.edu/cgi-bin/viewv ... /?view=tar

Then 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/

I'm planning to make 0.9.3 release of PyRx soon that will include these changes packaged in the installer.

Thank you for the feedback.
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