The Molecular Graphics Laboratory Forum

Hi all,
While trying to run prepare_ligand4.py, I received the following error:

Traceback (most recent call last):
File "/home/brittmc/tools/mgltools/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py", line 207, in <module>
if a.coords!=coord_dict[a]: bad_list.append(a)
KeyError: <Atom instance> 737_2YXJ:A:N3C1001:H27

The command I executed was:
python ~/tools/mgltools/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py -l 737_2YXJ.pdb -o baz.pdbqt -A hydrogens

It will run correctly if I leave off the "-A hydrogens"

The file version is:
prepare_ligand4.py,v 1.5.4.1 2009/04/15 17:41:57 rhuey

any thoughts?
thanks!
britt

Ok, I believe I found the problem...

prepare_ligand4.py makes a check at the end of the main routine for atoms in the molecule that were moved/added during the prepare process. It creates a dict of starting molecules and then checks each molecule at the end against the starting point.

I'm not sure if I'm ahead or behind on my python version, but the version I'm using 2.6.6 throws an error when an attempt is made to find a key in a dict object that doesn't exist. The function actually works, but you get an error reported...

britt

Whoops, I just tried to revive an old thread on this exact topic. I have the same problem and suspected the same thing as you (when I commented out that for loop it worked fine). Eagerly awaiting any suggestions for a fix...

Apparently the fix has been made. I just checked out the latest source and see that is the case.

britt