ADL: Hydrated Docking Problem

mllanos at mllanos at
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 step, where the program gives me this error when I try to run the full mode (-F) with DLG and files as input:

Traceback (most recent call last):
 File "./scripts/", line 1192, in <module>
 harvest, affinity = getpoints(grid, coord(w), distance = 1.0) # angstroms
 File "./scripts/", 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 script and Babel)

I'm using python interpreter from MGLtools

Thanks in advance
best regards
Manuel A. Llanos ( - Ph.D. Student
Laboratory of Bioactive Research and Development ( - LIDeB
Faculty of Exact Sciences - National University of La Plata - Argentina.

More information about the autodock mailing list