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