ADL: Ligand Files in Hydrated Docking Example

Edmund R Marinelli edmundmarinelli at
Sat Oct 17 21:19:45 PDT 2020

I examined the example for hydrated docking provided at the following link:

In the file set download for the example there are the following pdbqt files
for the ligand:  ligand_xray.pdbqt, ligand.pdbqt, ligand_xray_HYDRO.pdbqt
and ligand_HYDRO.pdbqt .   In the tutorial is stated:  "– This protocol
assumes all the files have been already prepared for a standard docking
protocol (i.e. ligand and receptor structures; GPF and DPF parameter
files)."  I would expect that in the prep of files for standard run one
should generate one pdbqt for the ligand and one for the receptor.  The I
would expect , based on my reading of the paper , that a hydrated ligand
file is needed.  That's two ligand files, which is understandable. 
Examining the ligand_xray.pdbqt and the ligand.pdbqt files shows that they
are the same with respect to torsions, but that the X, Y and Z coordinates
for ligand_pdbqt are displaced by about -18, -48 and +13.5 relative to those
of ligand_xray.pdbqt.  All charges are the same for both. The same
difference is found for ligand_xray_HYDRO.pdbqt and ligand_HYDRO.pdbqt . 
What is the need for what appears to be an extra set of ligand files (the
ligand_xray and ligand_xray_Hydro pdbqt files)?  It appears that only the
ligand_HYDRO.pdbqt file is used in the hydrated docking .  However I do not
understand why the HYDRO files are displaced so far from the coordinates
found for the ligand in the original pdb file.  Can you explain?   

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