AddH: hydrogens bonded to each other

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:/Trametes ligand/out2.pdb"

Chain information for out2.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select ::name="UNL"

8 atoms, 8 bonds, 1 residue, 1 model selected  

> select ~sel & ##selected

4593 atoms, 4707 bonds, 1 pseudobond, 503 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> save "D:/Trametes ligand/2CP/LIG.mol2"

> ui tool show "Add Hydrogens"

> addh #!1

Summary of feedback from adding hydrogens to out2.pdb #1  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
5 hydrogens added  
  

> save "D:/Trametes ligand/2CP/LIG.mol2"

> hide #!1 models

> show #!1 models

> delete atoms

> delete bonds

> open "D:/Trametes ligand/out2.pdb"

Chain information for out2.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select ::name="CU"

4 atoms, 4 residues, 1 model selected  

> select ::name="UNL"

8 atoms, 8 bonds, 1 residue, 1 model selected  

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

4589 atoms, 4707 bonds, 499 residues, 1 model selected  

> select ~sel

12 atoms, 8 bonds, 5 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to out2.pdb #1  
---  
notes | No usable SEQRES records for out2.pdb (#1) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: /A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A GLN 499  
Chain-final residues that are not actual C termini:  
412 hydrogen bonds  
2891 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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\tool.py", line 120, in add_charges  
self._finish_add_charge(residues)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\tool.py", line 142, in _finish_add_charge  
non_std = add_standard_charges(self.session, residues=residues, **params)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\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 ILE 63 HN bonded to non-
heavy atom /A ILE 63 1HN  
  
chimerax.add_charge.charge.ChargeError: Hydrogen /A ILE 63 HN bonded to non-
heavy atom /A ILE 63 1HN  
  
File "C:\Program Files\ChimeraX\bin\Lib\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.  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to out2.pdb #1  
---  
notes | No usable SEQRES records for out2.pdb (#1) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: /A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A GLN 499  
Chain-final residues that are not actual C termini:  
409 hydrogen bonds  
0 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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\tool.py", line 120, in add_charges  
self._finish_add_charge(residues)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\tool.py", line 142, in _finish_add_charge  
non_std = add_standard_charges(self.session, residues=residues, **params)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\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 ILE 63 HN bonded to non-
heavy atom /A ILE 63 1HN  
  
chimerax.add_charge.charge.ChargeError: Hydrogen /A ILE 63 HN bonded to non-
heavy atom /A ILE 63 1HN  
  
File "C:\Program Files\ChimeraX\bin\Lib\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: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) HD Graphics 620
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_IN.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Vostro 3584
OS: Microsoft Windows 10 Home Single Language (Build 19045)
Memory: 8,485,642,240
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-7020U CPU @ 2.30GHz
OSLanguage: en-US

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