ADL: Ligands and Hydrogens - please help me

kbarakat at kbarakat at
Sun Jun 28 08:05:32 PDT 2009


I am performing VS experiment. My plan is to re-score my top hits  
using MD simulations by applying more accurate binding energy analysis  
on the protein-top_hit complex. The problem is that: Autodock merges  
hydrogens during the docking procedure and it is hard to restore them  
with the correct protonation states after docking. Bagdevi "a member  
in the mailing list" has suggested modifying the options of the while preparing my ligands and set it to not merge  

He suggested: -l <ligand_file> -U lps

or -l <ligand_file> -U ''

This procedure worked fine in keeping the hydrogens during docking.  
However, the results are dramatically different with the  
merged-hydrogen-ligands showed close to experimental binding modes "by  
comparing docking poses to crystal structure". On the other hand, the  
other two procedures in preparing my ligands "namely -U lsp or -U ''"  
showed scattering in the rmsd clustering with no well-defined binding  

Is there a way to optimize the docking runs while keeping hydrogens  
during docking? or Do I miss something in my calculations?

Thanks for your time,

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