Opened 6 years ago

Closed 6 years ago

Last modified 6 years ago

#3050 closed defect (fixed)

OpenMM: User-supplied template does not match the residue

Reported by: didny1@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 0.91 (2019-10-05)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-10-05)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed 'ChimeraX_ISOLDE-1.0b4-cp37-cp37m-win_amd64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
c:\users\didny\appdata\local\ucsf\chimerax\cache\0.91\installers\chimerax_isolde-1.0b4-cp37-cp37m-win_amd64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b4)
(1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Clipper==0.10.* in
c:\users\didny\appdata\local\ucsf\chimerax\0.91\site-packages (from ChimeraX-
ISOLDE==1.0b4) (0.10.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.91 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b4)
(0.91)  
Installing collected packages: ChimeraX-ISOLDE  
Found existing installation: ChimeraX-ISOLDE 1.0b3.dev5  
Uninstalling ChimeraX-ISOLDE-1.0b3.dev5:  
Successfully uninstalled ChimeraX-ISOLDE-1.0b3.dev5  
Successfully installed ChimeraX-ISOLDE-1.0b4  
Lock 2142724852488 acquired on
C:\Users\didny\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache.lock  
Lock 2142724852488 released on
C:\Users\didny\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache.lock  
  

WARNING: You are using pip version 19.2.3, however version 20.0.2 is
available.  
You should consider upgrading via the 'python -m pip install --upgrade pip'
command.  
  

> open F:\cryoEM\UMOD\umod_fixedseq_cistem_172-isolde2.cif format mmCIF

Summary of feedback from opening
F:\cryoEM\UMOD\umod_fixedseq_cistem_172-isolde2.cif  
---  
warnings | Unknown polymer entity '1' near line 135  
Unknown polymer entity '2' near line 4075  
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "NAG" near line 6114  
Unknown polymer entity '3' near line 6170  
Atom H1 is not in the residue template for LEU #329 in chain A  
Atom H1 is not in the residue template for VAL #450 in chain B  
Atom H11 is not in the residue template for NAG #585 in chain B  
Atom H1 is not in the residue template for ALA #326 in chain C  
Atom HD2 is not in the residue template for ASN #396 in chain C  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for umod_fixedseq_cistem_172-isolde2.cif #1  
---  
Chain | Description  
A | ?  
B | ?  
C | ?  
  

> open F:/cryoEM/UMOD/denmod_map.ccp4

Opened denmod_map.ccp4, grid size 133,77,185, pixel 1.45, shown at level
0.235, step 1, values float32  

> toolshed show ISOLDE

> set selectionWidth 4

Chain information for umod_fixedseq_cistem_172-isolde2.cif  
---  
Chain | Description  
1.1/A | ?  
1.1/B | ?  
1.1/C | ?  
  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> clipper spotlight radius 24.00

> clipper spotlight radius 24.00

> select #1.1

7984 atoms, 8075 bonds, 338 pseudobonds, 6 models selected  

No template found for residue B585 (NAG)  

Excluding residue  
Traceback (most recent call last):  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1313, in __init__  
sim_params, residue_templates)  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1409, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\simtk\openmm\app\forcefield.py", line 1108, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_4YB does not match the residue 392
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2676, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2696, in start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 644, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2796, in _handle_bad_template  
self.start_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2706, in start_sim  
sm.start_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 653, in start_sim  
sh.start_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1555, in start_sim  
self._prepare_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1500, in
_prepare_sim  
self.initialize_implicit_solvent(params)  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2741, in
initialize_implicit_solvent  
gbforce.addParticles(params)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 9186, in <lambda>  
__getattr__ = lambda self, name: _swig_getattr(self, CustomGBForce, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 74, in _swig_getattr  
return _swig_getattr_nondynamic(self, class_type, name, 0)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 69, in _swig_getattr_nondynamic  
return object.__getattr__(self, name)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2676, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2706, in start_sim  
sm.start_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 653, in start_sim  
sh.start_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1555, in start_sim  
self._prepare_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1500, in
_prepare_sim  
self.initialize_implicit_solvent(params)  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2741, in
initialize_implicit_solvent  
gbforce.addParticles(params)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 9186, in <lambda>  
__getattr__ = lambda self, name: _swig_getattr(self, CustomGBForce, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 74, in _swig_getattr  
return _swig_getattr_nondynamic(self, class_type, name, 0)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 69, in _swig_getattr_nondynamic  
return object.__getattr__(self, name)  
  
See log for complete Python traceback.  
  

> select #1.1

7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected  

> select #1.1

7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected  

> select #1.1

7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected  

> select #1.1

7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected  

> select #1.1

7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected  

> select #1.1

7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected  
Traceback (most recent call last):  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2676, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2706, in start_sim  
sm.start_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 653, in start_sim  
sh.start_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1555, in start_sim  
self._prepare_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1500, in
_prepare_sim  
self.initialize_implicit_solvent(params)  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2741, in
initialize_implicit_solvent  
gbforce.addParticles(params)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 9186, in <lambda>  
__getattr__ = lambda self, name: _swig_getattr(self, CustomGBForce, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 74, in _swig_getattr  
return _swig_getattr_nondynamic(self, class_type, name, 0)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 69, in _swig_getattr_nondynamic  
return object.__getattr__(self, name)  
  
See log for complete Python traceback.  
  

> select #1.1

7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected  
Traceback (most recent call last):  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2676, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2706, in start_sim  
sm.start_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 653, in start_sim  
sh.start_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1555, in start_sim  
self._prepare_sim()  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1500, in
_prepare_sim  
self.initialize_implicit_solvent(params)  
File "C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2741, in
initialize_implicit_solvent  
gbforce.addParticles(params)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 9186, in <lambda>  
__getattr__ = lambda self, name: _swig_getattr(self, CustomGBForce, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 74, in _swig_getattr  
return _swig_getattr_nondynamic(self, class_type, name, 0)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\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: 3.3.0 NVIDIA 450.12
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (5)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → OpenMM: User-supplied template does not match the residue

comment:2 by Tristan Croll, 6 years ago

Status: assigned → accepted

The traceback should go away (and be replaced by a more useful error pointing you at the offending residue) if you update to the latest version. The most common cause of this problem is that the hydrogens on the sugar are wrong (this often happens if the starting geometry is bad, unfortunately). I'm planning to add some functionality to see if the only difference between the residue and its MD template are hydrogens and fix accordingly, but it's not there yet. If you can send me the coordinates at tic20@…, I'd be happy to help get them simulation-ready.

comment:3 by Tristan Croll, 6 years ago

Resolution: → fixed
Status: accepted → closed

The traceback is suppressed in more recent ISOLDE builds, so closing this as "fixed".

in reply to:  4 ; comment:4 by didny1@…, 6 years ago 

Thank so much for the reply. So both errors are gone when I updated
ChimeraX to 0.93 from 3rd of April. The problem with sugar stays, but then
I just exclude it from the simulation. Unfortunately, I cannot share the
file (at least not yet) due to the collaboration.

czw., 16 kwi 2020 o 19:18 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
napisał(a):

in reply to:  5 ; comment:5 by Tristan Croll, 6 years ago 

No problem. You might have more luck with the sugar if you do “addh template true” followed by just “addh”. If it still doesn’t work, show all the hydrogens (“show”) and look closely at the residue for both hydrogens that are there and shouldn’t be, and ones that should be there and aren’t. The first scenario is easier to deal with - just ctrl-click on the atom then “del selAtom”. The latter is a bit trickier - let me know if that’s your case and I’ll advise further.
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