ADL: Preparing a Ligand in Autodock

Raja S rs0504 at hotmail.com
Mon Mar 3 13:59:04 PST 2008


Hi all,
 
I am fairly new at using autodock. I have a few questions about running a docking.
 
I am trying to load a ligand into autodock. I drew my molecules in chemdraw and converted the cdx file into a pdb file using openbabel. I imported the file into autodock tools and followed the manual to set the torsion degrees, etc. After I saved it as a a PDBQT file, I got many errors and the file did not save correctly. 
 
I am wondering how to fix this problem. How do I import drawn molecules into Chemdraw? 
 
In Chemdraw, what 3D specification do I have to make? Do I need to specify the angles, bond lengths, etc?
 
Thanks in advance for all your help
 
Raja
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