ADL: Attempting to use AutoDockTools with protein structure containing Zn: It crashes...My mistake or a bug?
rhuey at scripps.edu
Tue Jan 8 06:49:13 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).
> --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---
Your problem probably is caused by an improper input file:
Specifically, the pdb standard requires that the names of atoms with
two-character elements start in column 12 (zero-based) and those of
one-character element in column 13. [I cannot be certain this is the
issue without looking at your file]
Here is a snippet of a pdb file showing a properly formatted ZN. Note
that the hydrogen H is in column 13 while the zinc Z is in column 12.
The pdb parser in ADT interprets a ZN starting in column 13 as an atom
of element "Z" (for which there is no information)
ATOM 4260 H1 ASN 285 50.523 49.273 69.914 0.00
ATOM 4265 ZN ZN 286 38.027 48.584 69.337 0.00
More information about the autodock