ChimeraX Log

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

alias cls close session

UCSF ChimeraX version: 1.12rc202606020412 (2026-06-02)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX

open 6i4q format mmcif fromDatabase pdbe_bio

Summary of feedback from opening 6i4q fetched from pdbe_bio
warnings	Missing or incorrect sequence information. Inferred polymer connectivity. Atom H is not in the residue template for VAL /B:-6

6i4q bioassembly 1 title:
Crystal structure of the human dihydrolipoamide dehydrogenase at 1.75 Angstrom resolution [more info...]

Chain information for 6i4q bioassembly 1 #1
Chain	Description
A	Dihydrolipoyl dehydrogenase, mitochondrial
B	Dihydrolipoyl dehydrogenase, mitochondrial

Non-standard residues in 6i4q bioassembly 1 #1
BTB — (BTB)
FAD — (FAD)
SO4 — (SO4)

249 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
Opened 1 biological assemblies for 6i4q

delete :btb

delete :so4

delete :hoh

altlocs change A

Changed 10 residues to alternate location A (10 residues were already A)

altlocs clean

Removed alternate locations from 20 residues

minimize

Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Deleting residues with incomplete backbones

Summary of feedback from adding hydrogens to 6i4q bioassembly 1 #1
notes	No usable SEQRES records for 6i4q bioassembly 1 (#1) chain A; guessing termini instead No usable SEQRES records for 6i4q bioassembly 1 (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A GLN 3 Chain-initial residues that are not actual N termini: /B VAL -6 Chain-final residues that are actual C termini: /A PHE 474, /B PHE 474 Chain-final residues that are not actual C termini: 903 hydrogen bonds 5 hydrogens added

Summary of feedback from adding hydrogens to 6i4q bioassembly 1 #1

notes

No usable SEQRES records for 6i4q bioassembly 1 (#1) chain A; guessing termini instead
No usable SEQRES records for 6i4q bioassembly 1 (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A GLN 3
Chain-initial residues that are not actual N termini: /B VAL -6
Chain-final residues that are actual C termini: /A PHE 474, /B PHE 474
Chain-final residues that are not actual C termini:
903 hydrogen bonds
5 hydrogens added

Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue FAD (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /tmp/tmp2_mx6xc5/ante.in.mol2 -fi mol2 -o /tmp/tmp2_mx6xc5/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(FAD)
(FAD) Welcome to antechamber 20.0: molecular input file processor.
(FAD)
(FAD) Info: Finished reading file (/tmp/tmp2_mx6xc5/ante.in.mol2); atoms read (85), bonds read (90).
(FAD) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(FAD)

Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(FAD)
(FAD)
(FAD) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(FAD) Info: Total number of electrons: 408; net charge: -1
(FAD)
(FAD) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(FAD)
(FAD)

Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1

(FAD)
(FAD)

Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

(FAD)
Charges for residue FAD determined
Dock prep finished
Traceback (most recent call last):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 322, in execute
    cmd.run(cmd_text)
  File "/usr/lib/ucsf-chimerax/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/lib/python3.11/site-packages/chimerax/minimize/cmd.py", line 43, in cmd_minimize
    dock_prep_caller(session, [structure], memorize_name="minimization", nogui=True,
  File "/usr/lib/ucsf-chimerax/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/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/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 132, in prep
    callback(session, state, structures)
  File "/usr/lib/ucsf-chimerax/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/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/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/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/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 156, in run_steps
    callback()
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 131, in <lambda>
    state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())
                                                            ^^^^
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/minimize/cmd.py", line 45, in <lambda>
    steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/minimize/cmd.py", line 232, in _minimize
    system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer, constraints=HBonds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/app/forcefield.py", line 1279, in createSystem
    data.setAtomClasses(self)
  File "/usr/lib/ucsf-chimerax/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/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/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_6i4q_altlocs_A.html