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PostPosted: Tue Jul 21, 2015 6:37 am 
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Hi everyone!

when I am trying to run autodock file "*.dpf" it shows an error as you can see in attached file.


Could someone please help me out here!


Thank you


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PostPosted: Tue Jul 21, 2015 3:08 pm 
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Apparently your file 'eugino1.pdbqt' is not a correctly formatted pdbqt file.
To pinpoint the problem(s) with it, please post it.
Also indicate how you created it...


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PostPosted: Wed Jul 22, 2015 7:07 am 
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Hi Ruth

Thank you for your reply.

I downloaded file from pubchem in *.sdf format (as *.pdb format was not available on pubchem site) and converted *.sdf format into *.pdb format using "Online SMILES Translator and Structure File Generator".

PDBQT file from the above pdb file was prepared using MGL tools -1.5.6 as follows:

1) LIGAND /INPUT/OPEN/euginol.pdb
following message shown:
summary for ligand
setup ligand:
added gasteiger charges
merged 11 non-polar hydrogens found
6 aromatic carbons detected 4 rotatable bonds set TORSDOF to 4


2) EDIT/DELETE/DELETE HYDROGENS
3) LIGAND/TORSION TREE/CHOOSE TORSION/DONE
3) LIGAND/OUTPUT/save as PDBQT

I don't know where am I going wrong.

Thank you
Ravindra


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PostPosted: Tue Aug 04, 2015 8:25 pm 
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Hi Ravindra,
In order to resolve the problem you report, please post the contents of your files: euginol.pdb and euginol.pdbqt.

Best wishes,
Ruth


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