id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7768 _openmm.new_Context: bad allocation 352884536@… Tristan Croll "{{{ 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 }}} " defect assigned normal Third Party Tom Goddard all ChimeraX