ADL: Attempting to use AutoDockTools with protein structure containing Zn: It crashes...My mistake or a bug?

David ccl_list at
Mon Jan 7 17:02:07 PST 2008


I'm trying to use AutoDock Tools to set up a docking run. My receptor 
protein has a Zn ion in it.
If I try to read in the pdb file through AutoDock tools (File->Read 
Molecule) and then attempt
to add hydrogens, I get a python error about

ValueError: Could not find atomic number for Z Z

Zn is in the parameters file used for autogrid and autodock, but doesn't 
seem to be in the
parameters list that is inherently used in ADT, and I can't figure out 
how to fix that (which
may mean, as the title says, I'm an idiot).

If I try to ignore the error, things just get worse (it won't add 
hydrogens, so flexible residue
assingments/assigning charges/etc. don't work).

Is there some trick to using Zn?

(emails appreciated, since I don't subscribe to this list).



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