_openmm.new_Context: bad allocation

[352884536@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "E:/c3a_c3ar/final model/antagonist/j54_dehZFLIP.mrc"

Opened j54_dehZFLIP.mrc, grid size 360,360,360, pixel 0.824, shown at level
0.000898, step 2, values float32  

> open "E:/c3a_c3ar/final model/antagonist/noligand.pdb"

Chain information for noligand.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> volume #1 step 1

> volume #1 level 0.04348

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for noligand.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
2.2/C | No description available  
  
Done loading forcefield  

> clipper associate #2 toModel #1

Invalid "toModel" argument: Must specify 1 structure, got 0 for "#1"  

> clipper associate #1 toModel #2

> isolde start

> addh

Summary of feedback from adding hydrogens to noligand.pdb #2.2  
---  
notes | No usable SEQRES records for noligand.pdb (#2.2) chain A; guessing
termini instead  
No usable SEQRES records for noligand.pdb (#2.2) chain B; guessing termini
instead  
No usable SEQRES records for noligand.pdb (#2.2) chain C; guessing termini
instead  
Chain-initial residues that are actual N termini: /A LEU 13, /B SER 1, /C SER
3  
Chain-initial residues that are not actual N termini: /A PRO 332, /A LYS 426  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ALA 560, /A GLY 173, /A
THR 411, /B GLY 214, /C SER 229  
493 hydrogen bonds  
Adding 'H' to /A LYS 426  
/A ALA 560 is not terminus, removing H atom from 'C'  
/A GLY 173 is not terminus, removing H atom from 'C'  
/A THR 411 is not terminus, removing H atom from 'C'  
/B GLY 214 is not terminus, removing H atom from 'C'  
/C SER 229 is not terminus, removing H atom from 'C'  
6333 hydrogens added  
  

> hide HC

> hide HC

> hide HC

> clipper spotlight radius 5.00

> clipper spotlight radius 50.00

> clipper spotlight radius 50.00

> hide HC

Traceback (most recent call last):  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 2735, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 2774, in start_sim  
sm.start_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 670, in start_sim  
sh.start_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1597, in start_sim  
self._prepare_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1558, in
_prepare_sim  
integrator, platform, properties)  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\simtk\openmm\app\simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6270, in __init__  
this = _openmm.new_Context(*args)  
Exception: bad allocation  
  
Exception: bad allocation  
  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6270, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 2735, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 2774, in start_sim  
sm.start_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 670, in start_sim  
sh.start_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1597, in start_sim  
self._prepare_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1558, in
_prepare_sim  
integrator, platform, properties)  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\simtk\openmm\app\simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6270, in __init__  
this = _openmm.new_Context(*args)  
Exception: bad allocation  
  
Exception: bad allocation  
  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6270, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1161, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1954, in
update_dihedral_restraints  
restraints.enableds, restraints.spring_constants, restraints.targets,
restraints.cutoffs)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 512.15
OpenGL renderer: NVIDIA GeForce GTX 1650 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: IPASON
Model:  
OS: Microsoft Windows 10 家庭中文版 (Build 19044)
Memory: 17,130,639,360
MaxProcessMemory: 137,438,953,344
CPU: 6 AMD Ryzen 5 3500X 6-Core Processor             "
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Tristan Croll]

Sorry for failing to respond at the time - I was in the process of changing jobs and a bit distracted. The first thing you should *definitely* do is upgrade to ChimeraX 1.5 - the version you're using is a year and a half old. Could you let me know if that fixes the problem?