ADL: Zero-Charge :[] in ligand_dict.py for charged ligands

Elena Dolghih ldolghih at gmail.com
Mon Jan 14 06:56:21 PST 2008


Hi,



I am following the virtual screening tutorial to create my own set of
ligands. So far I have two questions. After I ran prepare_ligand4.py script
and got my .pdbq files, I looked at ligand_dict.py output file. My ligands
have  unprotonated carboxylic group so the charge on them should be -1, but
in ligand_dict.py file they all have 'zero-charge': []  line. How come?
Since looking at each .pdbq file, all the atoms are assigned charges.  Another
question, where do I get examine_ligand_dict.py script? I found
prepare_ligand4.py and pythonsh scripts in
~/MGLToolsPckgs/AutoDockTools/Utilities24


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