id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2905 OpenMM: Multiple matching templates found for residue pett@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.91 (2019-12-23) 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 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:\Users\Lenye\Dropbox\thil > article-2020\Thiaminemonophosphatekinase_refine_44_dimer.pdb"" Summary of feedback from opening C:\Users\Lenye\Dropbox\thil article-2020\Thiaminemonophosphatekinase_refine_44_dimer.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2019-03-12 Time 15:04:44 South Africa Standard Time +0200 (155239588 Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : C:\Users\Lenye\Desktop\ThiL Molecular Replacement\over 29 messages similar to the above omitted Chain information for Thiaminemonophosphatekinase_refine_44_dimer.pdb #1 --- Chain | Description A B | No description available > isolde start > set selectionWidth 4 Chain information for Thiaminemonophosphatekinase_refine_44_dimer.pdb --- Chain | Description 1.1/A 1.1/B | No description available Done loading forcefield QWidget::repaint: Recursive repaint detected > addh Summary of feedback from adding hydrogens to Thiaminemonophosphatekinase_refine_44_dimer.pdb #1.1 --- notes | No usable SEQRES records for Thiaminemonophosphatekinase_refine_44_dimer.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for Thiaminemonophosphatekinase_refine_44_dimer.pdb (#1.1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 59, /B LEU 59 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A TYR 337, /B TYR 337 1210 hydrogen bonds /A TYR 337 is not terminus, removing H atom from 'C' /B TYR 337 is not terminus, removing H atom from 'C' 4490 hydrogens added > toolshed show ISOLDE > select 8790 atoms, 8574 bonds, 41 models selected Loading residue template for SO4 from internal database Traceback (most recent call last): File ""C:\Users\Lenye\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\Lenye\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\Lenye\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 609, in __init__ raise e File ""C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""C:\Users\Lenye\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\Lenye\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:\Users\Lenye\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 1117, in createSystem [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom, ignoreExternalBonds=ignoreExternalBonds) File ""C:\Users\Lenye\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 893, in _getResidueTemplateMatches raise Exception('Multiple matching templates found for residue %d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) Exception: Multiple matching templates found for residue 568 (HOH): OHE, GLYCAM_ROH. Exception: Multiple matching templates found for residue 568 (HOH): OHE, GLYCAM_ROH. File ""C:\Users\Lenye\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 893, in _getResidueTemplateMatches raise Exception('Multiple matching templates found for residue %d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\Lenye\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\Lenye\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\Lenye\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 609, in __init__ raise e File ""C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""C:\Users\Lenye\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\Lenye\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:\Users\Lenye\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 1117, in createSystem [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom, ignoreExternalBonds=ignoreExternalBonds) File ""C:\Users\Lenye\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 893, in _getResidueTemplateMatches raise Exception('Multiple matching templates found for residue %d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) Exception: Multiple matching templates found for residue 568 (HOH): OHE, GLYCAM_ROH. Exception: Multiple matching templates found for residue 568 (HOH): OHE, GLYCAM_ROH. File ""C:\Users\Lenye\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 893, in _getResidueTemplateMatches raise Exception('Multiple matching templates found for residue %d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\Lenye\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\Lenye\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\Lenye\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 609, in __init__ raise e File ""C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""C:\Users\Lenye\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\Lenye\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:\Users\Lenye\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 1117, in createSystem [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom, ignoreExternalBonds=ignoreExternalBonds) File ""C:\Users\Lenye\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 893, in _getResidueTemplateMatches raise Exception('Multiple matching templates found for residue %d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) Exception: Multiple matching templates found for residue 568 (HOH): OHE, GLYCAM_ROH. Exception: Multiple matching templates found for residue 568 (HOH): OHE, GLYCAM_ROH. File ""C:\Users\Lenye\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 893, in _getResidueTemplateMatches raise Exception('Multiple matching templates found for residue %d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) See log for complete Python traceback. > select :HOH 860 atoms, 572 bonds, 1 model selected > select :HOH 860 atoms, 572 bonds, 1 model selected > hide sel atoms > select :MG 4 atoms, 1 model selected > hide sel atoms > select :SO4 10 atoms, 8 bonds, 1 model selected > select clear > toolshed show ISOLDE > set selectionWidth 4 Done loading forcefield > select 8790 atoms, 8574 bonds, 47 models selected > select 8790 atoms, 8574 bonds, 47 models selected Loading residue template for SO4 from internal database Traceback (most recent call last): File ""C:\Users\Lenye\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\Lenye\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\Lenye\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 609, in __init__ raise e File ""C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""C:\Users\Lenye\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\Lenye\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:\Users\Lenye\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 1117, in createSystem [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom, ignoreExternalBonds=ignoreExternalBonds) File ""C:\Users\Lenye\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 893, in _getResidueTemplateMatches raise Exception('Multiple matching templates found for residue %d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) Exception: Multiple matching templates found for residue 568 (HOH): OHE, GLYCAM_ROH. Exception: Multiple matching templates found for residue 568 (HOH): OHE, GLYCAM_ROH. File ""C:\Users\Lenye\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 893, in _getResidueTemplateMatches raise Exception('Multiple matching templates found for residue %d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) See log for complete Python traceback. OpenGL version: 3.3.13542 Core Profile Forward-Compatible Context 25.20.14012.0 OpenGL renderer: AMD Radeon(TM) R2 Graphics OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Third Party fixed all ChimeraX