ADL: Ligands and hydrogens

kbarakat at kbarakat at
Tue Jun 23 15:13:23 PDT 2009


Is there a way to keep all hydrogens in the ligand.pdbqt files and not  
to merge non-polar hydrogens. My plan is to use Molecular Dynamics  
simulations to calculate the binding energies of several  
Receptor-Ligand complex starting from the proposed docked structures.  
My major problem in that is: AutoDock merge the hydrogens of the  
ligand and it's very hard to track them back to the initial  
protonation states even with programs like open babel.

Thanks for your time and your help is so much appreciated

With my best regards

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