ADL: Cannot determine the flexibility of my structure

Kann Vearasilp kann.vearasilp at
Thu Oct 25 12:08:32 PDT 2007

Hello all,

I am a graduate student who is beginning to work on  Autodock as a  
docking tools in my project. In essence, my protein structure, as a  
pdb file, has HEM atom inside the file. I am trying to determine the  
flexible residue in the stucture and ADT throws an error about cannot  
find the atom's atomic number.

ERROR *********************************************
Traceback (most recent call last):
   File "/Library/MGLTools/MGLToolsPckgs/ViewerFramework/", line  
685, in tryto
     result = apply( command, args, kw )
   File "/Library/MGLTools/MGLToolsPckgs/AutoDockTools/", line 219, in doit
   File "/Library/MGLTools/MGLToolsPckgs/AutoDockTools/", line 369, in setAutoDockElements
   File "/Library/MGLTools/MGLToolsPckgs/PyBabel/", line  
127, in assignHybridization
     a.babel_atomic_number = self.get_atomic_number(a.babel_type)
   File "/Library/MGLTools/MGLToolsPckgs/PyBabel/", line  
102, in get_atomic_number
     raise ValueError( "Could not find atomic number for %s %s"% \
ValueError: Could not find atomic number for Hm Hm

The system is Mac OS 10.4 and I am using ADT 1.4.4.

Does this mean that AutoDock cannot recognize my HEM atom in my pdb  
file? I can see that Autodock 4 supports Fe atom type in its  
parameter file. Should I make change in my PDB file to get support  
from Autodock?

Thank you very much in advance for any suggestion,


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