AddCharge: Hydrogen bonded to non-heavy atom

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.8.0-47-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7rc202312140717 (2023-12-14 07:17:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7rc202312140717 (2023-12-14)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/albert/ZINC20/ZINC20_mol2_test/DOCK6_10%_ligands/ligand_sampling_demo2/1_struct/7up1_H.pdb

Chain information for 7up1_H.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A ARG 270: phi -74.8, psi none trans  

/A SER 191 OG has bad number of bonds (3)  

Applying ARG rotamer (chi angles: -174.4 178.1 -63.4 105.1) to /A ARG 270  
Summary of feedback from adding hydrogens to 7up1_H.pdb #1  
---  
warnings | /A SER 191 OG has bad number of bonds (3)  
Skipped 8 atom(s) with bad connectivities; see log for details  
notes | No usable SEQRES records for 7up1_H.pdb (#1) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLU 30  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ARG 270  
Chain-final residues that are not actual C termini:  
Skipping possible acceptor with bad geometry: /A ASP 96 OD2  
Wrong number of grandchild atoms for phi/psi acceptor /A ASP 96 OD2  
  
Skipping possible acceptor with bad geometry: /A ASP 96 OD2  
Wrong number of grandchild atoms for phi/psi acceptor /A ASP 96 OD2  
  
Skipping possible acceptor with bad geometry: /A ASN 103 OD1  
Wrong number of grandchild atoms for phi/psi acceptor /A ASN 103 OD1  
  
Skipping possible acceptor with bad geometry: /A ASN 176 OD1  
Wrong number of grandchild atoms for phi/psi acceptor /A ASN 176 OD1  
  
Skipping possible acceptor with bad geometry: /A ASP 96 OD1  
Wrong number of grandchild atoms for phi/psi acceptor /A ASP 96 OD1  
  
3 messages similar to the above omitted  
196 hydrogen bonds  
63 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 120, in add_charges  
self._finish_add_charge(residues)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 142, in _finish_add_charge  
non_std = add_standard_charges(self.session, residues=residues, **params)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 127, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to non-heavy atom %s" % (h, heavy))  
chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 40 H06 bonded to non-
heavy atom /A GLU 40 HH  
  
chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 40 H06 bonded to non-
heavy atom /A GLU 40 HH  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 127, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to non-heavy atom %s" % (h, heavy))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 23.0.4-0ubuntu1~22.04.1
OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits)
OpenGL vendor: Mesa

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: innotek GmbH
Model: VirtualBox
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: oracle
CPU: 12 12th Gen Intel(R) Core(TM) i5-12500H
Cache Size: 18432 KB
Memory:
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	Mem:           6.6Gi       1.4Gi       3.5Gi        79Mi       1.7Gi       4.9Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
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[Eric Pettersen]

Bad CONECT records