CCL: Autodock Tools error - Undefined atom type Hm

From: "Ahmet Koseoglu" <naclcys+/-hotmail.com>
Subject: CCL: Autodock Tools error - Undefined atom type Hm
Date: Sat, 30 Oct 2010 15:19:12 -0400

 Sent to CCL by: "Ahmet  Koseoglu" [naclcys ~ hotmail.com]
 Dear CCL members,
 I have been trying to run Autodock for the first time using AutoDock Tools and
 Autodock4. I want to define flexible residues for  the receptor molecule but
 when I try to choose the residue by opening the receptor first (no probem up to
 here) and following the command Flexible Residues -> Input -> Choose
 Macromolecule it gives the following error:
 ERROR *********************************************
 Traceback (most recent call last):
   File "C:\Program Files\MGLTools
 1.5.4\MGLToolsPckgs\ViewerFramework\VF.py", line 735, in tryto
     result = apply( command, args, kw )
   File "C:\Program Files\MGLTools
 1.5.4\MGLToolsPckgs\AutoDockTools\autoflexCommands.py", line 235, in doit
     ad4_typer.setAutoDockElements(mol)
   File "C:\Program Files\MGLTools
 1.5.4\MGLToolsPckgs\AutoDockTools\atomTypeTools.py", line 369, in
 setAutoDockElements
     ah.assignHybridization(mol.allAtoms)
   File "C:\Program Files\MGLTools
 1.5.4\MGLToolsPckgs\PyBabel\atomTypes.py", line 127, in assignHybridization
     a.babel_atomic_number = self.get_atomic_number(a.babel_type)
   File "C:\Program Files\MGLTools
 1.5.4\MGLToolsPckgs\PyBabel\atomTypes.py", line 103, in get_atomic_number
     (name,_name) )
 ValueError: Could not find atomic number for Hm Hm
 Now I figured these hydrogens are the the ones on the methyl groups that are
 attached to the HEME group and are written as HMA1, HMA2, HMA3, HMB1,... so on
 in the PDB file. As far as I understand the progam does not recognize the
 hydrogen type "HM". I don't know with which symbol I can replace HM in
 the PDB input or if there is any other solution. Any help is appreciated.
 Regards,
 Ahmet Koseoglu