ADL: Hydrated Docking Problem

mllanos at biol.unlp.edu.ar mllanos at biol.unlp.edu.ar
Wed Aug 19 09:36:37 PDT 2020


Hi all,
I'm having some problems trying to use the hydrated docking protocol
It works fine until the dry.py step, where the program gives me this error when I try to run the full mode (-F) with DLG and W.map files as input:

Traceback (most recent call last):
 File "./scripts/dry.py", line 1192, in <module>
 harvest, affinity = getpoints(grid, coord(w), distance = 1.0) # angstroms
 File "./scripts/dry.py", line 737, in getpoints
 harvesting.append( data[z,y,x] )
IndexError: index (53) out of range (0<=index<53) in dimension 1

If I run it with option -E (extract only LE pose, no LCLE) it works, but the generated PDBQT file can not converted back to PDB (I've tried with pdbqt_to_pdb.py script and Babel)

I'm using python interpreter from MGLtools

Thanks in advance
best regards
Manuel A. Llanos (http://www.linkedin.com/in/manuel-augusto-llanos/?locale=en_US) - Ph.D. Student
Laboratory of Bioactive Research and Development (http://lideb.biol.unlp.edu.ar/) - LIDeB
Faculty of Exact Sciences - National University of La Plata - Argentina.


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