ChimeraX Log

Startup Messages
warning No presets found in custom preset folder /home/paul/config/chimerax

alias cls close session
alias cls close session
UCSF ChimeraX version: 1.13.dev202606032116 (2026-06-03)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
open 7wgr format mmcif fromDatabase pdbe_bio
open 7wgr format mmcif fromDatabase pdbe_bio
Summary of feedback from opening 7wgr fetched from pdbe_bio
warning Missing or incorrect sequence information. Inferred polymer connectivity.

7wgr bioassembly 1 title:
Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) component of the human alpha-ketoglutarate (2-oxoglutarate) dehydrogenase complex [more info...]

Chain information for 7wgr bioassembly 1 #1
Chain Description
A B 2-oxoglutarate dehydrogenase, mitochondrial

Non-standard residues in 7wgr bioassembly 1 #1
CA — (CA)
MG — (MG)
TPP — (TPP)

Computing secondary structure
Opened 1 biological assemblies for 7wgr
minimize dockPrep true acMethod gasteiger
minimize dockPrep true acMethod gasteiger
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Deleting residues with incomplete backbones
Filling out missing side chains
/A ASP 170: phi -76.3, psi -19.1 trans
/A SER 1023: phi -92.9, psi none trans
/B ASP 170: phi -76.3, psi -19.7 trans
/B SER 1023: phi -96.4, psi none trans
Applying ASP rotamer (chi angles: 60.4 -13.5) to /A ASP 170
Applying SER rotamer (chi angles: 65.3) to /A SER 1023
Applying ASP rotamer (chi angles: 60.4 -13.5) to /B ASP 170
Applying SER rotamer (chi angles: 65.3) to /B SER 1023
Summary of feedback from adding hydrogens to 7wgr bioassembly 1 #1
notes No usable SEQRES records for 7wgr bioassembly 1 (#1) chain A; guessing termini instead
No usable SEQRES records for 7wgr bioassembly 1 (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A ALA 129, /B ALA 129
Chain-initial residues that are not actual N termini: /A ASN 365, /A MET 602, /B ASN 365, /B MET 602
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A SER 1023, /A ASP 346, /A LYS 574, /B SER 1023, /B ASP 346, /B LYS 574
1249 hydrogen bonds
Adding 'H' to /A ASN 365
Adding 'H' to /A MET 602
Adding 'H' to /B ASN 365
Adding 'H' to /B MET 602
/A SER 1023 is not terminus, removing H atom from 'C'
/B SER 1023 is not terminus, removing H atom from 'C'
13388 hydrogens added

Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue TPP (net charge -2) with gasteiger method
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber -i /tmp/tmpnzwl1mel/ante.in.mol2 -fi mol2 -o /tmp/tmpnzwl1mel/ante.out.mol2 -fo mol2 -c gas -nc -2 -j 5 -s 2 -dr n
(TPP)
(TPP) Welcome to antechamber 20.0: molecular input file processor.
(TPP)
(TPP) Info: Finished reading file (/tmp/tmpnzwl1mel/ante.in.mol2); atoms read (42), bonds read (43).
(TPP) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(TPP)
(TPP)
(TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d /usr/lib/ucsf-chimerax-daily/bin/amber20/dat/antechamber/ATOMTYPE_GAS.DEF
(TPP)
(TPP) Warning: The net charge of the molecule (-2 ) does not equal the total formal charge (-3.00) according to the Gasteiger atom types.
(TPP)
Charges for residue TPP determined
Dock prep finished
Traceback (most recent call last):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 322, in execute
    cmd.run(cmd_text)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3245, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/minimize/cmd.py", line 57, in cmd_minimize
    dock_prep_caller(session, [structure], memorize_name="minimization", nogui=True,
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller
    run_steps(session, state, structures)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 161, in run_steps
    step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'],
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 150, in prep
    callback(session, state, structures)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 161, in run_steps
    step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'],
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep
    callback(session, state, structures)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 161, in run_steps
    step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'],
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep
    callback(session, state, structures)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 156, in run_steps
    callback()
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 149, in <lambda>
    state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())
                                                            ^^^^
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/minimize/cmd.py", line 59, in <lambda>
    steps=max_steps: _minimize(ses, struct, fixed, updates, log, steps), **kw)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/minimize/cmd.py", line 262, in _minimize
    system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer, constraints=HBonds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/openmm/app/forcefield.py", line 1279, in createSystem
    data.setAtomClasses(self)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/openmm/app/forcefield.py", line 683, in setAtomClasses
    self.atomClasses = [classNameForType[self.atomType[atom]] for atom in self.atoms]
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/openmm/app/forcefield.py", line 683, in <listcomp>
    self.atomClasses = [classNameForType[self.atomType[atom]] for atom in self.atoms]
                        ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
KeyError: 'N'

KeyError: 'N'

File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/openmm/app/forcefield.py", line 683, in
self.atomClasses = [classNameForType[self.atomType[atom]] for atom in self.atoms]
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^

See log for complete Python traceback.

log save log_minimize_7wgr.html
log save log_minimize_7wgr.html