Charge-determination convergence failure for 4pk2

[kristen.browne@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.dev202210260016 (2022-10-26 00:16:05 UTC)
Description
loaded attached file and ran coulombic preset.
Maybe related to issue #8028 that is already reported

Log:
UCSF ChimeraX version: 1.6.dev202210260016 (2022-10-26)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/brownekm/Downloads/2fae-assembly-1.cif

mmCIF parsing error: unexpected data value near line 1  

> open C:/Users/brownekm/Downloads/4pk2.pdb

4pk2.pdb title:  
Tubulin acetyltransferase complex with bisubstrate analog [more info...]  
  
Chain information for 4pk2.pdb #1  
---  
Chain | Description | UniProt  
A | α-tubulin N-acetyltransferase 1 | ATAT_HUMAN  
B | acetyl-ser-(N-propanoyl-lys)-asp--THR-NH2 peptide |  
  
Non-standard residues in 4pk2.pdb #1  
---  
ACE — acetyl group  
COA — coenzyme A  
NH2 — amino group  
PRK — N~6~-propanoyl-L-lysine (N(6)-propionyllysine)  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 3379 atom radii, 3166 bond radii, 1 pseudobond radii  
Changed 1 pseudobond dash  

> set bgColor #ffffff00

Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Summary of feedback from adding hydrogens to 4pk2.pdb #1  
---  
warnings | Not adding hydrogens to /A VAL 37 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A GLU 111 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 150 CD because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 174 CD because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 187 CD because it is missing heavy-atom bond
partners  
notes | Termini for 4pk2.pdb (#1) chain A determined from SEQRES records  
Termini for 4pk2.pdb (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /A PHE -1, /B ACE 1  
Chain-initial residues that are not actual N termini: /A VAL 37  
Chain-final residues that are actual C termini: /A PRO 196, /B NH2 6  
Chain-final residues that are not actual C termini: /A ALA 26  
Missing OXT added to C-terminal residue /A PRO 196  
159 hydrogen bonds  
Adding 'H' to /A VAL 37  
68 hydrogens added  
  

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A VAL 37  
/A GLU 111  
/A GLU 150  
/A GLU 174  
/A GLU 187  

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue PRK+COA (net charge -4) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmpzkjf0p5e\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpzkjf0p5e\ante.out.mol2 -fo mol2 -c
bcc -nc -4 -j 5 -s 2 -dr n  
(PRK+COA) ``  
(PRK+COA) `Welcome to antechamber 20.0: molecular input file processor.`  
(PRK+COA) ``  
(PRK+COA) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmpzkjf0p5e\ante.in.mol2); atoms read
(119), bonds read (121).`  
(PRK+COA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(PRK+COA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(PRK+COA) `bash.exe: warning: could not find /tmp, please create!`  
(PRK+COA) ``  
(PRK+COA) ``  
(PRK+COA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(PRK+COA) `bash.exe: warning: could not find /tmp, please create!`  
(PRK+COA) `Info: Total number of electrons: 538; net charge: -4`  
(PRK+COA) ``  
(PRK+COA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(PRK+COA) `bash.exe: warning: could not find /tmp, please create!`  
(PRK+COA) `/usr/bin/antechamber: Fatal Error!`  
(PRK+COA) `Cannot properly run ""C:/Program
Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out".`  
Failure running ANTECHAMBER for residue PRK+COA  
Check reply log for details  




OpenGL version: 3.3.0 NVIDIA 466.47
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP Z4 G4 Workstation
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 137,220,087,808
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) i9-10900X CPU @ 3.70GHz
OSLanguage: en-US

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File attachment: 4pk2.pdb

4pk2.pdb​

[kristen.browne@…]

Added by email2trac

[Eric Pettersen]

The charge determination works with the Gasteiger method, and therefore will work with the latest version of the presets.