Good morning, I'm trying to do some modeling on a molecule. However I'dont understand why, when I open the .dlg file on PyMol to see the poses, my molecule has a "=O-CH3" binding instead of a "-O-CH3". I'have already checked the pdb file, which I prepared using Spartan and looks correct, same as the PDBQT. I opened both files using PyMol and the molecule is correct
Abanish Biswas
First convert the structure from smiles to mol2 format. Then convert the mol2 file to pdbqt in Autodock. Hope this will work.
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Alessio Sanfilippo
Abanish Biswas Thank you for your answering, sorry but I'm new into this so I have to ask you.. If i convert smiles to pdbqt, it works but I'm not doing an accurate energy minimization (am I correct?)
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