virtual screening for many ligands of Zinc database

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virtual screening for many ligands of Zinc database

Postby elahe » Thu Aug 18, 2016 3:08 pm

hello
hope you well
we want to perform structure-based approach to mine the ZINC database by virtual screening to identify novel inhibitor for a protein. we downloaded sdf files from ZINC database but we don't know that how these files should be imported by openbable option in PyRx . Each of the sdf files that have been downloaded from Zinc database contains many ligands (about 147000). Is it possible to import these files by openbabel option in pyrx?
please guide me.
many thanks in advance
best
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elahe
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Re: virtual screening for many ligands of Zinc database

Postby sargis » Sun Sep 18, 2016 6:08 am

Hello, hope you are well too.

You can import sdf files and convert them to pdbqt as shown in https://www.youtube.com/watch?v=niw6gHDLfO4

Please let me know if you have questions or need more information.

Thank you for using PyRx!
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Re: virtual screening for many ligands of Zinc database

Postby elahe » Tue Sep 20, 2016 6:15 am

hi
Thank you for your kindness
Previous problem was solved, but I have a new problem.
About a day after the implementation of Vina program, it was stopped. I've repeated several times this program and and I got following error:
(pythonw.exe has stopped working:
A problem caused the program to stop working correctly, Windows will close the program and notify you if a solution is available.)
please help me to solve this problem
thank you sincerely
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Re: virtual screening for many ligands of Zinc database

Postby sargis » Wed Sep 21, 2016 11:01 am

You are welcome, glad previous problem was solved. For the new problem, please let me know the version of PyRx you are using. Also, upload all the input pdbqt files. I'm pretty sure Windows will not notify you if a solution is available:-( but someone in this forum might be able to help.
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