OpenMM: No template found for residue

[mks131@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 96, in __exit__  
os.replace(self._tmp_filename, self.name)  
PermissionError: [WinError 32] The process cannot access the file because it
is being used by another process:
'C:\\\Users\\\Manoj\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\ModelPanel-1.tmp' ->
'C:\\\Users\\\Manoj\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\ModelPanel-1'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 621, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1613, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\model_panel\\__init__.py", line 21, in start_tool  
return model_panel(session, tool_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 345, in model_panel  
_mp = ModelPanel(session, tool_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 29, in __init__  
now = self.settings.last_use = time()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\settings.py", line 190, in __setattr__  
ConfigFile.__setattr__(self, name, value)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\configfile.py", line 365, in __setattr__  
ConfigFile.save(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\configfile.py", line 315, in save  
self._config.write(f)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 98, in __exit__  
os.remove(self._tmp_filename)  
FileNotFoundError: [WinError 2] The system cannot find the file specified:
'C:\\\Users\\\Manoj\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\ModelPanel-1.tmp'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 426, in start_tools  
bi.start_tool(session, tool_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Model Panel
in bundle ChimeraX-ModelPanel:  
[WinError 2] The system cannot find the file specified:
'C:\\\Users\\\Manoj\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\ModelPanel-1.tmp'  
  
Tool "Model Panel" failed to start:  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Model Panel
in bundle ChimeraX-ModelPanel:  
[WinError 2] The system cannot find the file specified:
'C:\\\Users\\\Manoj\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\ModelPanel-1.tmp'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\Users\Manoj\Downloads\relion_postprocess_job126_masked_refined_pixelsize.ccp4
> format ccp4

Opened relion_postprocess_job126_masked_refined_pixelsize.ccp4, grid size
376,376,376, pixel 0.649, shown at level 0.00472, step 2, values float32  

> volume #1 level 0.009646

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> clipper spotlight radius 13.00

> clipper spotlight radius 40.00

Traceback (most recent call last):  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 1271, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 1297, in add_xtal_data  
map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\clipper\symmetry.py", line 174, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create,
auto_add_to_session=auto_add_to_session)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\clipper\symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\clipper\symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\clipper\symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 1271, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 1297, in add_xtal_data  
map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\clipper\symmetry.py", line 174, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create,
auto_add_to_session=auto_add_to_session)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\clipper\symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\clipper\symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\clipper\symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
  
See log for complete Python traceback.  
  

> open2 C:/Users/Manoj/Documents/phenix_lin28/lin28b_DNA.pdb

Chain information for lin28b_DNA.pdb #2  
---  
Chain | Description  
I | No description available  
J | No description available  
  
Chain information for lin28b_DNA.pdb  
---  
Chain | Description  
2.2/I | No description available  
2.2/J | No description available  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 652, in
_rebuild_molecule  
hide_residues = make_ladder(nd, residues, mol._ladder_params)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 1237, in make_ladder  
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 733, in get_cylinder  
h = distance(p0, p1)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\vector.py", line 71, in distance  
return sqrt(distance_squared(p, q))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\vector.py", line 63, in distance_squared  
if len(p) == 3:  
TypeError: object of type 'NoneType' has no len()  
  
Error processing trigger "changes":  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\vector.py", line 63, in distance_squared  
if len(p) == 3:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 525, in rebuild  
_rebuild_molecule('internal', mol)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 652, in
_rebuild_molecule  
hide_residues = make_ladder(nd, residues, mol._ladder_params)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 1237, in make_ladder  
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 733, in get_cylinder  
h = distance(p0, p1)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\vector.py", line 71, in distance  
return sqrt(distance_squared(p, q))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\vector.py", line 63, in distance_squared  
if len(p) == 3:  
TypeError: object of type 'NoneType' has no len()  
  
Error processing trigger "new frame":  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\vector.py", line 63, in distance_squared  
if len(p) == 3:  
  
See log for complete Python traceback.  
  

No template found for residue I-64 (DT)  

Adding hydrogens  
Summary of feedback from adding hydrogens to lin28b_DNA.pdb #2.2  
---  
notes | No usable SEQRES records for lin28b_DNA.pdb (#2.2) chain I; guessing
termini instead  
No usable SEQRES records for lin28b_DNA.pdb (#2.2) chain J; guessing termini
instead  
Chain-initial residues that are actual N termini: /I DT -64, /J DG -72  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /I DC 72, /J DA 64  
Chain-final residues that are not actual C termini:  
384 hydrogen bonds  
3098 hydrogens added  
  

No template found for residue I-64 (DT)  

Excluding residue  
Traceback (most recent call last):  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1424, 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 1147, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (DT). The set of atoms is similar
to DT, but it is missing 12 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1424, 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 1147, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (DT). The set of atoms matches
DT3, but the bonds are different. Perhaps the chain is missing a terminal
group?  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2699, in start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 597, in __init__  
self._parse_auto_template_error(e)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 647, in
_parse_auto_template_error  
self.isolde._handle_bad_template(residue)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2791, in _handle_bad_template  
self.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2699, in start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 597, in __init__  
self._parse_auto_template_error(e)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 647, in
_parse_auto_template_error  
self.isolde._handle_bad_template(residue)  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2709, in start_sim  
sm.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 667, in start_sim  
sh.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1570, in start_sim  
self._prepare_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1531, in
_prepare_sim  
integrator, platform, properties)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\simtk\openmm\app\simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6265, in __init__  
this = _openmm.new_Context(*args)  
Exception: Error creating array TabulatedFunction: clCreateBuffer (-61)  
  
Exception: Error creating array TabulatedFunction: clCreateBuffer (-61)  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6265, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.4531
OpenGL renderer: Intel(R) HD Graphics 5500
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Inspiron 7348
OS: Microsoft Windows 10 Home (Build 18362)
Memory: 8,501,149,696
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-5500U CPU @ 2.40GHz"

[Tristan Croll]

Two separate issues here. The problem with the missing template is *probably* due to a spurious hydrogen that sometimes gets added to the terminal phosphorus of nucleic acids (I'm just about ready to release a new ISOLDE version that will help a lot with problems like that).

The more interesting one is your final error:
Exception: Error creating array TabulatedFunction: clCreateBuffer (-61)

-61 is CL_INVALID_BUFFER_SIZE, which can be thrown if the buffer size is either zero or larger than CL_DEVICE_MAX_MEM_ALLOC_SIZE for your GPU. It's possible that the first case could happen if you have a map associated with your model, but the section of model you've selected to simulate is entirely outside of the map (this scenario is fixed in the coming new version). The other scenario is more difficult - unfortunately for this the only solution I can offer right now is "get a better GPU". ISOLDE's simulations are entirely dependent on GPU computing, and it tends to assume you have a compute-oriented GPU installed.

[Tristan Croll]

Clearing out the backlog of old tickets which (for various reasons) I forgot to close at the time - template issues like this are long since handled.