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 Post subject: sdf file format to pdbqt
PostPosted: Fri Aug 14, 2009 9:27 pm 
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Hi

I am trying to create pdbqt file from the sdf file format.

How can I do that using autodock utility tools? It seems works only for mol2 format, I do have sdf file more than 10000.

Thanks a lot, appreciate if any one suggest me the way to convert all sdf to pdbqt format.

venkat


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PostPosted: Tue Aug 18, 2009 2:28 pm 
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Hi all

I did posted question on 14th. Seems like either is not active or I posted in wrong place ?

Please someone can let me know if there is any active forum that could covers the autodock and mgltool queries that
could get some attention from the reader.

thanks
venkat


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PostPosted: Wed Aug 19, 2009 3:47 pm 
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You can use openbabel: see http://openbabel.org/wiki/Main_Page
I think you'll need to pass the -m flag to the program to get multiple mol2 output files:

babel -isdf sdfarchivename.sdf -omol2 outputname.mol2 -m

Then you can process the mol2 files with ADT's python scripts.

I would also recommend ChemAxon's JChem suite: http://www.chemaxon.com/
This has a nice conversion utility called molconvert.


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PostPosted: Thu Aug 20, 2009 7:38 pm 
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Thanks.

I did tried babel, it kind of getting halt and did not do multiple files either.

I thought there could be python script could convert all the sdf file with same ligand prefix as in sdf.

Thanks again for suggestion

Venkat


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