OpenMM: gbforce.addParticles: AttributeError

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-24)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warnings | 'clip' is a prefix of an existing command 'clipper'  
'rota' is a prefix of an existing command 'rotamers'  
  
UCSF ChimeraX version: 0.91 (2019-09-24)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open mnosym-init-001.pdb

Chain information for mnosym-init-001.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E | No description available  
F | No description available  
  

> open postmap_704_4_51.mrc

Opened postmap_704_4_51.mrc, grid size 240,240,240, pixel 1.56, shown at level
0.00874, step 1, values float32  

> isolde start

> set selectionWidth 4

Chain information for mnosym-init-001.pdb  
---  
Chain | Description  
1.1/A | No description available  
1.1/B | No description available  
1.1/C | No description available  
1.1/D 1.1/E | No description available  
1.1/F | No description available  
  
Done loading forcefield  

> set bgColor white

> clipper associate #2 toModel #1.1

> select clear

> addh

Summary of feedback from adding hydrogens to mnosym-init-001.pdb #1.1  
---  
notes | No usable SEQRES records for mnosym-init-001.pdb (#1.1) chain A;
guessing termini instead  
No usable SEQRES records for mnosym-init-001.pdb (#1.1) chain B; guessing
termini instead  
No usable SEQRES records for mnosym-init-001.pdb (#1.1) chain C; guessing
termini instead  
No usable SEQRES records for mnosym-init-001.pdb (#1.1) chain D; guessing
termini instead  
No usable SEQRES records for mnosym-init-001.pdb (#1.1) chain E; guessing
termini instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A LEU 198, /B SER 197, /C
ASN 199, /D GLU 196, /E GLU 196, /F ASN 199  
Chain-initial residues that are not actual N termini: /A ASP 725, /B ASP 725,
/C ILE 437, /C ASP 725, /D ASP 725, /E ASP 725, /F ASP 725  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ARG 772, /A SER 718, /B
PHE 771, /B SER 718, /C PHE 773, /C LEU 429, /C SER 718, /D ARG 772, /D SER
718, /E ARG 772, /E SER 718, /F GLY 767, /F SER 718  
2330 hydrogen bonds  
Adding 'H' to /A ASP 725  
Adding 'H' to /B ASP 725  
Adding 'H' to /C ILE 437  
Adding 'H' to /C ASP 725  
Adding 'H' to /D ASP 725  
2 messages similar to the above omitted  
/A ARG 772 is not terminus, removing H atom from 'C'  
/A SER 718 is not terminus, removing H atom from 'C'  
/B PHE 771 is not terminus, removing H atom from 'C'  
/B SER 718 is not terminus, removing H atom from 'C'  
/C PHE 773 is not terminus, removing H atom from 'C'  
8 messages similar to the above omitted  
26806 hydrogens added  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 2676, in _start_sim_or_toggle_pause  
self.start_sim()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 2706, in start_sim  
sm.start_sim()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 653, in start_sim  
sh.start_sim()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1552, in start_sim  
self._prepare_sim()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1497, in
_prepare_sim  
self.initialize_implicit_solvent(params)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 2738, in
initialize_implicit_solvent  
gbforce.addParticles(params)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 9186, in <lambda>  
__getattr__ = lambda self, name: _swig_getattr(self, CustomGBForce, name)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 74, in _swig_getattr  
return _swig_getattr_nondynamic(self, class_type, name, 0)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 69, in _swig_getattr_nondynamic  
return object.__getattr__(self, name)  
AttributeError: type object 'object' has no attribute '__getattr__'  
  
AttributeError: type object 'object' has no attribute '__getattr__'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 69, in _swig_getattr_nondynamic  
return object.__getattr__(self, name)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon HD - FirePro D300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tristan Croll]

Long since fixed - the user has an old, mid-development build of ChimeraX 0.91 prior to a change in the OpenMM library.