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Opened 6 years ago
Closed 6 years ago
#2470 closed defect (not a bug)
ISOLDE delayed reaction: Error invoking kernel computeBondedForces
| Reported by: | 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: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-08-27) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-08-27) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "/Volumes/ComplexI/Hannah Bridges/Work Folder/cryo- EM/deactive_mouse/postprocess_deactive.mrc" Opened postprocess_deactive.mrc, grid size 360,360,360, pixel 1.35, shown at level 0.0174, step 2, values float32 > open "/Volumes/ComplexI/Hannah Bridges/Work Folder/cryo- EM/deactive_mouse/Mouse-d-coot-9.pdb" Chain information for Mouse-d-coot-9.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available > hide #!2 models > show #!2 models > close #2 > open "/Volumes/ComplexI/Hannah Bridges/Work Folder/cryo- EM/deactive_mouse/Mouse-d-coot-9_real_space_refined.pdb" Chain information for Mouse-d-coot-9_real_space_refined.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available > toolshed show ISOLDE > set selectionWidth 4 Chain information for Mouse-d-coot-9_real_space_refined.pdb --- Chain | Description 2.3/A | No description available 2.3/B | No description available 2.3/C | No description available 2.3/D | No description available 2.3/E | No description available 2.3/F | No description available 2.3/G | No description available 2.3/H | No description available 2.3/I | No description available 2.3/J | No description available 2.3/K | No description available 2.3/L | No description available 2.3/M | No description available 2.3/N | No description available 2.3/O | No description available 2.3/P | No description available 2.3/Q | No description available 2.3/R | No description available 2.3/S | No description available 2.3/T | No description available 2.3/U | No description available 2.3/V | No description available 2.3/W | No description available 2.3/X | No description available 2.3/Y | No description available 2.3/Z | No description available 2.3/a | No description available 2.3/b | No description available 2.3/c | No description available 2.3/d | No description available 2.3/e | No description available 2.3/f | No description available 2.3/g | No description available 2.3/h | No description available 2.3/i | No description available 2.3/j | No description available 2.3/k | No description available 2.3/l | No description available 2.3/m | No description available 2.3/n | No description available 2.3/o | No description available 2.3/p | No description available 2.3/q | No description available 2.3/r | No description available 2.3/s | No description available Done loading forcefield Loading residue template for 3PE from internal database Loading residue template for ADP from internal database Loading residue template for AME from internal database Loading residue template for EHZ from internal database Loading residue template for FMN from internal database Loading residue template for PC1 from internal database Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: match Excluding residue Bad residue number: 92 Excluding residue Bad residue number: 246 Excluding residue Bad residue number: 536 Excluding residue Bad residue number: 881 Excluding residue Bad residue number: 1093 Excluding residue Bad residue number: 1521 Excluding residue Bad residue number: 2529 Excluding residue Bad residue number: 3583 Excluding residue Bad residue number: 3583 Excluding residue Bad residue number: 3583 Excluding residue Bad residue number: 4045 Excluding residue Bad residue number: 4959 Excluding residue Bad residue number: 5003 Adding hydrogens Summary of feedback from adding hydrogens to Mouse-d- coot-9_real_space_refined.pdb #2.3 --- warnings | Not adding hydrogens to /D LYS 40 CB because it is missing heavy- atom bond partners Not adding hydrogens to /D GLU 41 CB because it is missing heavy-atom bond partners Not adding hydrogens to /D LYS 42 CB because it is missing heavy-atom bond partners Not adding hydrogens to /I LYS 8 CB because it is missing heavy-atom bond partners Not adding hydrogens to /I GLU 9 CB because it is missing heavy-atom bond partners 18 messages similar to the above omitted Unknown hybridization for atoms (S2, S1, S3, S4) of residue type SF4; not adding hydrogens to them Unknown hybridization for atom (OG) of residue type SER; not adding hydrogens to it notes | No usable SEQRES records for Mouse-d-coot-9_real_space_refined.pdb (#2.3) chain A; guessing termini instead No usable SEQRES records for Mouse-d-coot-9_real_space_refined.pdb (#2.3) chain B; guessing termini instead No usable SEQRES records for Mouse-d-coot-9_real_space_refined.pdb (#2.3) chain C; guessing termini instead No usable SEQRES records for Mouse-d-coot-9_real_space_refined.pdb (#2.3) chain D; guessing termini instead No usable SEQRES records for Mouse-d-coot-9_real_space_refined.pdb (#2.3) chain E; guessing termini instead 40 messages similar to the above omitted Chain-initial residues that are actual N termini: /A FME 1, /B ARG 35, /C ARG 8, /D ALA 1, /E ALA 5, /F THR 10, /G SER 6, /H FME 1, /I THR 1, /J FME 1, /K FME 1, /L FME 1, /M FME 1, /N FME 1, /O LEU 1, /P LEU 1, /Q GLN 9, /R GLY 1, /S GLY 14, /T GLY 10, /U SER 1, /V LEU 4, /W THR 17, /X PRO 1, /Y VAL 1, /Z VAL 5, /a MET 1, /b AYA 1, /c PHE 2, /d MET 1, /e PRO 1, /f PHE 3, /g THR 21, /h LYS 6, /i SAC 1, /j ALA 6, /k GLY 17, /l HIS 2, /m LYS 4, /n ALA 1, /o ALA 2, /p TRP 4, /r AYA 1, /s THR 29 Chain-initial residues that are not actual N termini: /A PRO 50, /P THR 279, /P THR 334, /i TYR 64, /q GLU 2, /r GLU 90 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLU 115, /A PRO 25, /B ARG 189, /C GLU 214, /D ARG 430, /E GLY 216, /F HIS 437, /G GLU 693, /H MET 318, /I ARG 178, /J ARG 171, /K CYS 98, /L LEU 606, /M MET 459, /N ILE 344, /O LYS 320, /P TYR 342, /P THR 249, /P THR 323, /Q LYS 133, /R HIS 95, /S SER 95, /T ASP 82, /U GLU 88, /V ILE 115, /W PRO 130, /X VAL 171, /Y VAL 140, /Z THR 143, /a ASP 69, /b LEU 83, /c LEU 48, /d VAL 119, /e ARG 104, /f THR 54, /g ASP 121, /h ASN 143, /i HIS 127, /i PRO 35, /j PRO 68, /k ASP 94, /l ILE 157, /m TYR 128, /n ARG 176, /o ALA 115, /p GLN 171, /q TYR 144, /r LEU 112, /r ALA 74, /s ARG 68 5634 hydrogen bonds Adding 'H' to /P THR 279 Adding 'H' to /P THR 334 Adding 'H' to /i TYR 64 Adding 'H' to /q GLU 2 Adding 'H' to /r GLU 90 /A GLU 115 is not terminus, removing H atom from 'C' /A PRO 25 is not terminus, removing H atom from 'C' /B ARG 189 is not terminus, removing H atom from 'C' /C GLU 214 is not terminus, removing H atom from 'C' /D ARG 430 is not terminus, removing H atom from 'C' 45 messages similar to the above omitted 154 hydrogens added Bad residue number: match Excluding residue Bad residue number: 6221 Excluding residue Traceback (most recent call last): File "/Users/hrb/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Users/hrb/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/delayed_reaction.py", line 65, in callback self.ff(*self.ff_args) File "/Users/hrb/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1586, in _update_coordinates_and_repeat self.atoms.coords = th.coords File "/Users/hrb/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords f(self._c_pointer, n, pointer(coords)) RuntimeError: Error invoking kernel computeBondedForces: clEnqueueNDRangeKernel (-4) Error processing trigger "new frame": RuntimeError: Error invoking kernel computeBondedForces: clEnqueueNDRangeKernel (-4) File "/Users/hrb/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords f(self._c_pointer, n, pointer(coords)) See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.10.12 OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200 OpenGL vendor: Intel Inc.
Change History (3)
comment:1 by , 6 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE delayed reaction: Error invoking kernel computeBondedForces |
comment:3 by , 6 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
This construct is now up and running smoothly on a GPU workstation.
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