[Chimera-users] Error while using minimize

Andres Benitez andresbenitez at gmail.com
Fri Feb 9 17:50:02 PST 2018


I am trying to use minimize to resolve side chain positions which were
mutated using pymol. The file is saved as a pdb, but I am getting errors
when I try to use the minimize function. I am wondering if the error is
because the structure has some loops removed, or if there is something else
going on. I've attached the chimera session file and a text file with the
errors I am getting.


Andres Benitez
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180209/02ec9c7d/attachment.html>
-------------- next part --------------
No incomplete side chains
No SEQRES records for DRD2_withLIGAND_mutated.pdb (#0) chain A; guessing terminii instead
Chain-initial residues that are actual N terminii: HIS 33.A
Chain-initial residues that are not actual N terminii: 
Chain-final residues that are actual C terminii: 
Chain-final residues that are not actual C terminii: ILE 431.A
189 hydrogen bonds
Removing spurious proton from 'C' of ILE 431.A
Hydrogens added
Charge model: AMBER ff14SB
Non-standard atom names:
	ILE HD3 (ILE 45.A HD3, ILE 73.A HD3, ILE 109.A HD3 + 19 others)
	ILE HD1 (ILE 45.A HD1, ILE 73.A HD1, ILE 109.A HD1 + 19 others)
	ILE HD2 (ILE 45.A HD2, ILE 73.A HD2, ILE 109.A HD2 + 19 others)
Total charge for #0: -0.228
The following residues had non-integral charges:
	ILE 45.A -0.0558
	ILE 73.A -0.0558
	ILE 109.A -0.0558
	ILE 122.A -0.0558
	ILE 128.A -0.0558
	ILE 130.A -0.0558
	ILE 156.A -0.0558
	ILE 158.A -0.0558
	ILE 166.A -0.0558
	ILE 203.A -0.0558
	ILE 210.A -0.0558
	ILE 212.A -0.0558
	ILE 214.A -0.0558
	ILE 377.A -0.0558
	ILE 383.A -0.0558
	ILE 384.A -0.0558
	ILE 391.A -0.0558
	ILE 394.A -0.0558
	ILE 397.A -0.0558
	ILE 424.A -0.0558
	ILE 425.A -0.0558
	ILE 431.A -0.0558
Correct charges are unknown for 3 non-standard atom names in otherwise standard residues

Charges of 0.0 were assigned to the unknown atoms

1 model(s) had non-integral total charge
Details in reply log

AttributeError Exception in Tk callback
  Function: <function command at 0x11c7f76e0> (type: <type 'function'>)
  Module: <module 'chimera.baseDialog' from '/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.pyc'> (line: 447)
  Args: ()
Traceback (innermost last):
  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1747, in __call__
    return apply(self.func, args)
  File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 449, in command
    getattr(s, buttonFuncName(txt))()
  File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 704, in OK
  File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/gui.py", line 88, in Apply
    status=chimera.replyobj.status, **settings), self.process)
  File "/Applications/Chimera.app/Contents/Resources/share/AddH/gui.py", line 353, in checkNoHyds
  File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/gui.py", line 88, in <lambda>
    status=chimera.replyobj.status, **settings), self.process)
  File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 133, in initiateAddCharges
    doneCB(unchargedResidues, unchargedAtoms)
  File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 127, in doneCB
    cb(ur, ua)
  File "/Applications/Chimera.app/Contents/Resources/share/DockPrep/__init__.py", line 287, in <lambda>
    _chargeCB(ur, uc, m, **kw))
  File "/Applications/Chimera.app/Contents/Resources/share/DockPrep/__init__.py", line 292, in _chargeCB
    _postAddCharge(mols, **kw)
  File "/Applications/Chimera.app/Contents/Resources/share/DockPrep/__init__.py", line 303, in _postAddCharge
  File "/Applications/Chimera.app/Contents/Resources/share/MMMD/MMTKinter.py", line 143, in _finishDockPrep
  File "/Applications/Chimera.app/Contents/Resources/share/MMMD/MMTKinter.py", line 58, in _finishInit
  File "/Applications/Chimera.app/Contents/Resources/share/MMMD/MMTKinter.py", line 195, in _makeMmtkMolecules
  File "/Applications/Chimera.app/Contents/Resources/share/MMMD/MMTKinter.py", line 485, in __init__
    self._makeStandardResidue(molGroup, r, *v)
  File "/Applications/Chimera.app/Contents/Resources/share/MMMD/MMTKinter.py", line 561, in _makeStandardResidue
    self._addStandardResidue(molGroup, mg, chimera2mmtk)
  File "/Applications/Chimera.app/Contents/Resources/share/MMMD/MMTKinter.py", line 692, in _addStandardResidue
    "amber_atom_type": a.gaffType,
AttributeError: '_molecule.Atom' object has no attribute 'gaffType'

AttributeError: '_molecule.Atom' object has no attribute 'gaffType'

  File "/Applications/Chimera.app/Contents/Resources/share/MMMD/MMTKinter.py", line 692, in _addStandardResidue
    "amber_atom_type": a.gaffType,

See reply log for Python traceback.

-------------- next part --------------
A non-text attachment was scrubbed...
Name: DRD2_mutated.py
Type: text/x-python-script
Size: 300062 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180209/02ec9c7d/attachment.bin>

More information about the Chimera-users mailing list