From owner-chemistry@ccl.net Sat Oct 30 15:50:01 2010 From: "Ahmet Koseoglu naclcys__hotmail.com" To: CCL Subject: CCL: Autodock Tools error - Undefined atom type Hm Message-Id: <-43040-101030151914-23945-sGUO2sZgdih+gQ+9RbyHhg---server.ccl.net> X-Original-From: "Ahmet Koseoglu" 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