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#3592 closed defect (fixed)

Template mismatch errors

Reported by:	kartik.manne@…	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:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open2 "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/ReadySet_21/588AMS-
> CH235p12-M5-293_apply_ncs_17.updated-coot-1.updated.pdb"

Chain information for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated.pdb #1  
---  
Chain | Description  
A F K | No description available  
A F K | No description available  
B G L | No description available  
C H M | No description available  
D I N | No description available  
  

> set bgColor white

> addh

Summary of feedback from adding hydrogens to 588AMS-
CH235p12-M5-293_apply_ncs_17.updated-coot-1.updated.pdb #1  
---  
notes | No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_17.updated-coot-1.updated.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated.pdb (#1) chain B; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated.pdb (#1) chain C; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated.pdb (#1) chain D; guessing termini instead  
10 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A NAG 528, /A NAG 504, /B
VAL 518, /C GLN 1, /D GLU 1, /F NAG 528, /F NAG 504, /G VAL 518, /H GLN 1, /I
GLU 1, /K NAG 528, /K NAG 504, /L VAL 518, /M GLN 1, /N GLU 1  
Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157,
/A GLY 312, /A ASN 409, /A NAG 516, /A NAG 520, /A NAG 523, /B GLY 572, /C GLY
134, /F THR 71, /F CYS 157, /F GLY 312, /F ASN 409, /F NAG 516, /F NAG 520, /F
NAG 523, /G GLY 572, /H GLY 134, /K THR 71, /K CYS 157, /K GLY 312, /K ASN
409, /K NAG 516, /K NAG 520, /K NAG 523, /L GLY 572, /M GLY 134  
Chain-final residues that are actual C termini: /A BMA 525, /F BMA 525, /K BMA
525  
Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A
ASN 147, /A ILE 309, /A ASN 398, /A MAN 510, /A BMA 518, /A NAG 521, /B ASP
664, /B SER 546, /C CYS 216, /C SER 128, /D GLY 212, /F VAL 503, /F GLU 62, /F
ASN 147, /F ILE 309, /F ASN 398, /F MAN 510, /F BMA 518, /F NAG 521, /G ASP
664, /G SER 546, /H CYS 216, /H SER 128, /I GLY 212, /K VAL 503, /K GLU 62, /K
ASN 147, /K ILE 309, /K ASN 398, /K MAN 510, /K BMA 518, /K NAG 521, /L ASP
664, /L SER 546, /M CYS 216, /M SER 128, /N GLY 212  
2449 hydrogen bonds  
/A VAL 503 is not terminus, removing H atom from 'C'  
/A GLU 62 is not terminus, removing H atom from 'C'  
/A ASN 147 is not terminus, removing H atom from 'C'  
/A ILE 309 is not terminus, removing H atom from 'C'  
/A ASN 398 is not terminus, removing H atom from 'C'  
25 messages similar to the above omitted  
68 hydrogens added  
  

> open2 "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/cryosparc_P41_J32_009_volume_map_sharp_local.mrc"

Opened cryosparc_P41_J32_009_volume_map_sharp_local.mrc, grid size
320,320,320, pixel 1.07, shown at level 0.659, step 2, values float32  

> volume #2 step 1

> clipper associate #2 toModel #1

Chain information for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated.pdb  
---  
Chain | Description  
1.2/A 1.2/F 1.2/K | No description available  
1.2/A 1.2/F 1.2/K | No description available  
1.2/B 1.2/G 1.2/L | No description available  
1.2/C 1.2/H 1.2/M | No description available  
1.2/D 1.2/I 1.2/N | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> clipper spotlight radius 32.00

> show cartoons

> hide atoms

> hide #1.3 models

> show #1.3 models

> hide #1.3 models

> show #1.3 models

> hide #1.3 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.1 models

> show cartoons

> show cartoons

> show cartoons

QWidget::repaint: Recursive repaint detected  

> show #!1.1 models

No template found for residue A526 (NAG)  

Excluding residue  

No template found for residue F160 (ASN)  

Excluding residue  

No template found for residue F392 (ASN)  

Excluding residue  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 95
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_NLN does not match the residue 253
(ASN)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_NLN does not match the residue 495
(ASN)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__  
raise e  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem  
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
ignoreExternalBonds=ignoreExternalBonds)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 618 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
Exception: Multiple matching templates found for residue 618 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__  
raise e  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem  
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
ignoreExternalBonds=ignoreExternalBonds)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 626 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
Exception: Multiple matching templates found for residue 626 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__  
raise e  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem  
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
ignoreExternalBonds=ignoreExternalBonds)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 645 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
Exception: Multiple matching templates found for residue 645 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__  
raise e  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem  
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
ignoreExternalBonds=ignoreExternalBonds)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 656 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
Exception: Multiple matching templates found for residue 656 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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.  
  

> close session

Deleting atomic symmetry model...  

> open2 "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/ReadySet_21/588AMS-
> CH235p12-M5-293_apply_ncs_17.updated-coot-1.updated.pdb"

Chain information for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated.pdb #1  
---  
Chain | Description  
A F K | No description available  
A F K | No description available  
B G L | No description available  
C H M | No description available  
D I N | No description available  
  
Chain information for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated.pdb  
---  
Chain | Description  
1.2/A 1.2/F 1.2/K | No description available  
1.2/A 1.2/F 1.2/K | No description available  
1.2/B 1.2/G 1.2/L | No description available  
1.2/C 1.2/H 1.2/M | No description available  
1.2/D 1.2/I 1.2/N | No description available  
  

> addh

Summary of feedback from adding hydrogens to 588AMS-
CH235p12-M5-293_apply_ncs_17.updated-coot-1.updated.pdb #1.2  
---  
notes | No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_17.updated-coot-1.updated.pdb (#1.2) chain A;
guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated.pdb (#1.2) chain B; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated.pdb (#1.2) chain C; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated.pdb (#1.2) chain D; guessing termini instead  
10 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A NAG 528, /A NAG 504, /B
VAL 518, /C GLN 1, /D GLU 1, /F NAG 528, /F NAG 504, /G VAL 518, /H GLN 1, /I
GLU 1, /K NAG 528, /K NAG 504, /L VAL 518, /M GLN 1, /N GLU 1  
Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157,
/A GLY 312, /A ASN 409, /A NAG 516, /A NAG 520, /A NAG 523, /B GLY 572, /C GLY
134, /F THR 71, /F CYS 157, /F GLY 312, /F ASN 409, /F NAG 516, /F NAG 520, /F
NAG 523, /G GLY 572, /H GLY 134, /K THR 71, /K CYS 157, /K GLY 312, /K ASN
409, /K NAG 516, /K NAG 520, /K NAG 523, /L GLY 572, /M GLY 134  
Chain-final residues that are actual C termini: /A BMA 525, /F BMA 525, /K BMA
525  
Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A
ASN 147, /A ILE 309, /A ASN 398, /A MAN 510, /A BMA 518, /A NAG 521, /B ASP
664, /B SER 546, /C CYS 216, /C SER 128, /D GLY 212, /F VAL 503, /F GLU 62, /F
ASN 147, /F ILE 309, /F ASN 398, /F MAN 510, /F BMA 518, /F NAG 521, /G ASP
664, /G SER 546, /H CYS 216, /H SER 128, /I GLY 212, /K VAL 503, /K GLU 62, /K
ASN 147, /K ILE 309, /K ASN 398, /K MAN 510, /K BMA 518, /K NAG 521, /L ASP
664, /L SER 546, /M CYS 216, /M SER 128, /N GLY 212  
2449 hydrogen bonds  
/A VAL 503 is not terminus, removing H atom from 'C'  
/A GLU 62 is not terminus, removing H atom from 'C'  
/A ASN 147 is not terminus, removing H atom from 'C'  
/A ILE 309 is not terminus, removing H atom from 'C'  
/A ASN 398 is not terminus, removing H atom from 'C'  
25 messages similar to the above omitted  
68 hydrogens added  
  

> open2 "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/cryosparc_P41_J32_009_volume_map_sharp_local.mrc"

Opened cryosparc_P41_J32_009_volume_map_sharp_local.mrc, grid size
320,320,320, pixel 1.07, shown at level 0.659, step 2, values float32  

> volume #2 step 1

> clipper associate #2 toModel #1

> hide #!1.2 models

> show #!1.2 models

> hide #!1.1 models

> show cartoons

> hide atoms

> show #!1.1 models

> show atoms

> hide atoms

> show sel atoms

> select clear

> hide atoms

> show atoms

No template found for residue K392 (ASN)  

Excluding residue  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_NLN does not match the residue 128
(ASN)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__  
raise e  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem  
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
ignoreExternalBonds=ignoreExternalBonds)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 237 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
Exception: Multiple matching templates found for residue 237 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 #1

47996 atoms, 48507 bonds, 77 pseudobonds, 19 models selected  

No template found for residue A160 (ASN)  

Excluding residue  

No template found for residue A392 (ASN)  

Excluding residue  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_NLN does not match the residue 112
(ASN)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_NLN does not match the residue 341
(ASN)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__  
raise e  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem  
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
ignoreExternalBonds=ignoreExternalBonds)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 442 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
Exception: Multiple matching templates found for residue 442 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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.  
  

Failed to send bug report. Error while sending follows:  

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit  
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/chimerax/webservices/post_form.py", line 40, in
post_multipart_formdata  
h.request('POST', url, body=body, headers=headers)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/http/client.py", line
1252, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/http/client.py", line
1298, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/http/client.py", line
1247, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/http/client.py", line
1026, in _send_output  
self.send(msg)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/http/client.py", line
966, in send  
self.connect()  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/http/client.py", line
938, in connect  
(self.host,self.port), self.timeout, self.source_address)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/socket.py", line 728,
in create_connection  
raise err  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/socket.py", line 716,
in create_connection  
sock.connect(sa)  
ConnectionRefusedError: [Errno 111] Connection refused  

Failed to send bug report. Error while sending follows:  

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit  
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/chimerax/webservices/post_form.py", line 40, in
post_multipart_formdata  
h.request('POST', url, body=body, headers=headers)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/http/client.py", line
1252, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/http/client.py", line
1298, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/http/client.py", line
1247, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/http/client.py", line
1026, in _send_output  
self.send(msg)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/http/client.py", line
966, in send  
self.connect()  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/http/client.py", line
938, in connect  
(self.host,self.port), self.timeout, self.source_address)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/socket.py", line 728,
in create_connection  
raise err  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/socket.py", line 716,
in create_connection  
sock.connect(sa)  
ConnectionRefusedError: [Errno 111] Connection refused  

> close session

Deleting atomic symmetry model...  

> open2 "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/588AMS-
> CH235p12-M5-293_apply_ncs_17.updated-coot-1.pdb"

Chain information for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-coot-1.pdb
#1  
---  
Chain | Description  
A K | No description available  
A | No description available  
B G L | No description available  
C H M | No description available  
D I N | No description available  
F | No description available  
F K | No description available  
  
Chain information for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-coot-1.pdb  
---  
Chain | Description  
1.2/A 1.2/K | No description available  
1.2/A | No description available  
1.2/B 1.2/G 1.2/L | No description available  
1.2/C 1.2/H 1.2/M | No description available  
1.2/D 1.2/I 1.2/N | No description available  
1.2/F | No description available  
1.2/F 1.2/K | No description available  
  

> open2 "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/cryosparc_P41_J32_009_volume_map_sharp_local.mrc"

Opened cryosparc_P41_J32_009_volume_map_sharp_local.mrc, grid size
320,320,320, pixel 1.07, shown at level 0.659, step 2, values float32  

> volume #2 step 1

> addh

Summary of feedback from adding hydrogens to 588AMS-
CH235p12-M5-293_apply_ncs_17.updated-coot-1.pdb #1.2  
---  
notes | No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_17.updated-coot-1.pdb (#1.2) chain A; guessing
termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.pdb (#1.2) chain B; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.pdb (#1.2) chain C; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.pdb (#1.2) chain D; guessing termini instead  
10 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A NAG 528, /A NAG 504, /B
VAL 518, /C GLN 1, /D GLU 1, /F NAG 527, /F NAG 504, /G VAL 518, /H GLN 1, /I
GLU 1, /K NAG 528, /K NAG 504, /L VAL 518, /M GLN 1, /N GLU 1  
Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157,
/A GLY 312, /A ASN 409, /A NAG 516, /A NAG 520, /B GLY 572, /C GLY 134, /F THR
71, /F CYS 157, /F GLY 312, /F ASN 409, /F NAG 516, /F NAG 520, /G GLY 572, /H
GLY 134, /K THR 71, /K CYS 157, /K GLY 312, /K ASN 409, /K NAG 516, /K NAG
520, /L GLY 572, /M GLY 134  
Chain-final residues that are actual C termini: /A NAG 527, /F NAG 526, /K NAG
526  
Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A
ASN 147, /A ILE 309, /A ASN 398, /A MAN 510, /A BMA 518, /B ASP 664, /B SER
546, /C CYS 216, /C SER 128, /D GLY 212, /F VAL 503, /F GLU 62, /F ASN 147, /F
ILE 309, /F ASN 398, /F MAN 510, /F BMA 518, /G ASP 664, /G SER 546, /H CYS
216, /H SER 128, /I GLY 212, /K VAL 503, /K GLU 62, /K ASN 147, /K ILE 309, /K
ASN 398, /K MAN 510, /K BMA 518, /L ASP 664, /L SER 546, /M CYS 216, /M SER
128, /N GLY 212  
2461 hydrogen bonds  
/A VAL 503 is not terminus, removing H atom from 'C'  
/A GLU 62 is not terminus, removing H atom from 'C'  
/A ASN 147 is not terminus, removing H atom from 'C'  
/A ILE 309 is not terminus, removing H atom from 'C'  
/A ASN 398 is not terminus, removing H atom from 'C'  
25 messages similar to the above omitted  
75 hydrogens added  
  

> clipper associate #2 toModel #1

> select #1

48000 atoms, 48507 bonds, 84 pseudobonds, 13 models selected  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__  
raise e  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem  
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
ignoreExternalBonds=ignoreExternalBonds)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 444 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
Exception: Multiple matching templates found for residue 444 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__  
raise e  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem  
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
ignoreExternalBonds=ignoreExternalBonds)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 444 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
Exception: Multiple matching templates found for residue 444 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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.  
  

> close session

Deleting atomic symmetry model...  

> open2 "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/RealSpaceRefine_24/588AMS-
> CH235p12-M5-293_apply_ncs_17.updated-coot-1.updated-
> rsr24_real_space_refined.cif"

Summary of feedback from opening /home/kartikmanne/Documents/CH235
structures/588AMS_CH235.12-M5-293/RealSpaceRefine_24/588AMS-
CH235p12-M5-293_apply_ncs_17.updated-coot-1.updated-
rsr24_real_space_refined.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 1464  
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "NAG" near line 1510  
Missing entity information. Treating each chain as a separate entity.  
Missing second residue in struct_conn "C00001"  
Missing second residue in struct_conn "C00002"  
Missing second residue in struct_conn "C00003"  
Missing second residue in struct_conn "C00004"  
Missing second residue in struct_conn "C00005"  
1 messages similar to the above omitted  
Missing first residue in struct_conn "C00007"  
Missing first residue in struct_conn "C00008"  
Missing first residue in struct_conn "C00009"  
Missing first residue in struct_conn "C00010"  
Missing first residue in struct_conn "C00011"  
8 messages similar to the above omitted  
Missing second residue in struct_conn "C00020"  
Missing first residue in struct_conn "C00021"  
Missing first residue in struct_conn "C00022"  
Missing first residue in struct_conn "C00023"  
Missing first residue in struct_conn "C00024"  
Missing first residue in struct_conn "C00025"  
1 messages similar to the above omitted  
Missing second residue in struct_conn "C00027"  
Missing first residue in struct_conn "C00028"  
Missing first residue in struct_conn "C00029"  
Missing first residue in struct_conn "C00030"  
Missing first residue in struct_conn "C00031"  
Missing first residue in struct_conn "C00032"  
15 messages similar to the above omitted  
Missing second residue in struct_conn "C00048"  
Missing first residue in struct_conn "C00049"  
Missing first residue in struct_conn "C00050"  
Missing first residue in struct_conn "C00051"  
Missing first residue in struct_conn "C00052"  
Missing first residue in struct_conn "C00053"  
4 messages similar to the above omitted  
Missing second residue in struct_conn "C00058"  
Missing second residue in struct_conn "C00059"  
Missing first residue in struct_conn "C00060"  
Missing first residue in struct_conn "C00061"  
Missing first residue in struct_conn "C00062"  
Missing first residue in struct_conn "C00063"  
Missing first residue in struct_conn "C00064"  
Missing second residue in struct_conn "C00065"  
Missing second residue in struct_conn "C00066"  
Missing first residue in struct_conn "C00067"  
Missing first residue in struct_conn "C00068"  
Missing first residue in struct_conn "C00069"  
Missing first residue in struct_conn "C00070"  
Missing first residue in struct_conn "C00071"  
7 messages similar to the above omitted  
Missing second residue in struct_conn "C00079"  
Missing first residue in struct_conn "C00080"  
Missing first residue in struct_conn "C00081"  
Missing first residue in struct_conn "C00082"  
Missing first residue in struct_conn "C00083"  
Missing first residue in struct_conn "C00084"  
7 messages similar to the above omitted  
Missing second residue in struct_conn "C00092"  
Missing second residue in struct_conn "C00093"  
Missing first residue in struct_conn "C00094"  
Missing first residue in struct_conn "C00095"  
Missing first residue in struct_conn "C00096"  
Missing first residue in struct_conn "C00097"  
Missing first residue in struct_conn "C00098"  
41 messages similar to the above omitted  
Missing second residue in struct_conn "C00143"  
Missing second residue in struct_conn "C00144"  
Missing second residue in struct_conn "C00145"  
Missing second residue in struct_conn "C00146"  
Missing second residue in struct_conn "C00147"  
11 messages similar to the above omitted  
Missing first residue in struct_conn "C00162"  
Missing first residue in struct_conn "C00163"  
Missing first residue in struct_conn "C00164"  
Missing first residue in struct_conn "C00165"  
Missing first residue in struct_conn "C00166"  
33 messages similar to the above omitted  
Missing second residue in struct_conn "C00222"  
Missing second residue in struct_conn "C00223"  
Missing first residue in struct_conn "C00224"  
Missing first residue in struct_conn "C00225"  
Missing first residue in struct_conn "C00226"  
Missing first residue in struct_conn "C00227"  
Missing first residue in struct_conn "C00228"  
16 messages similar to the above omitted  
Missing second residue in struct_conn "C00245"  
Missing second residue in struct_conn "C00246"  
Missing second residue in struct_conn "C00247"  
Missing second residue in struct_conn "C00248"  
Missing second residue in struct_conn "C00249"  
1 messages similar to the above omitted  
Missing first residue in struct_conn "C00251"  
Missing first residue in struct_conn "C00252"  
Missing first residue in struct_conn "C00253"  
Missing first residue in struct_conn "C00254"  
Missing first residue in struct_conn "C00255"  
8 messages similar to the above omitted  
Missing second residue in struct_conn "C00264"  
Missing first residue in struct_conn "C00265"  
Missing first residue in struct_conn "C00266"  
Missing first residue in struct_conn "C00267"  
Missing first residue in struct_conn "C00268"  
Missing first residue in struct_conn "C00269"  
1 messages similar to the above omitted  
Missing second residue in struct_conn "C00271"  
Missing first residue in struct_conn "C00272"  
Missing first residue in struct_conn "C00273"  
Missing first residue in struct_conn "C00274"  
Missing first residue in struct_conn "C00275"  
Missing first residue in struct_conn "C00276"  
15 messages similar to the above omitted  
Missing second residue in struct_conn "C00292"  
Missing first residue in struct_conn "C00293"  
Missing first residue in struct_conn "C00294"  
Missing first residue in struct_conn "C00295"  
Missing first residue in struct_conn "C00296"  
Missing first residue in struct_conn "C00297"  
4 messages similar to the above omitted  
Missing second residue in struct_conn "C00302"  
Missing second residue in struct_conn "C00303"  
Missing first residue in struct_conn "C00304"  
Missing first residue in struct_conn "C00305"  
Missing first residue in struct_conn "C00306"  
Missing first residue in struct_conn "C00307"  
Missing first residue in struct_conn "C00308"  
Missing second residue in struct_conn "C00309"  
Missing second residue in struct_conn "C00310"  
Missing first residue in struct_conn "C00311"  
Missing first residue in struct_conn "C00312"  
Missing first residue in struct_conn "C00313"  
Missing first residue in struct_conn "C00314"  
Missing first residue in struct_conn "C00315"  
7 messages similar to the above omitted  
Missing second residue in struct_conn "C00323"  
Missing first residue in struct_conn "C00324"  
Missing first residue in struct_conn "C00325"  
Missing first residue in struct_conn "C00326"  
Missing first residue in struct_conn "C00327"  
Missing first residue in struct_conn "C00328"  
7 messages similar to the above omitted  
Missing second residue in struct_conn "C00336"  
Missing second residue in struct_conn "C00337"  
Missing first residue in struct_conn "C00338"  
Missing first residue in struct_conn "C00339"  
Missing first residue in struct_conn "C00340"  
Missing first residue in struct_conn "C00341"  
Missing first residue in struct_conn "C00342"  
41 messages similar to the above omitted  
Missing second residue in struct_conn "C00387"  
Missing second residue in struct_conn "C00388"  
Missing second residue in struct_conn "C00389"  
Missing second residue in struct_conn "C00390"  
Missing second residue in struct_conn "C00391"  
11 messages similar to the above omitted  
Missing first residue in struct_conn "C00406"  
Missing first residue in struct_conn "C00407"  
Missing first residue in struct_conn "C00408"  
Missing first residue in struct_conn "C00409"  
Missing first residue in struct_conn "C00410"  
33 messages similar to the above omitted  
Missing second residue in struct_conn "C00466"  
Missing second residue in struct_conn "C00467"  
Missing first residue in struct_conn "C00468"  
Missing first residue in struct_conn "C00469"  
Missing first residue in struct_conn "C00470"  
Missing first residue in struct_conn "C00471"  
Missing first residue in struct_conn "C00472"  
16 messages similar to the above omitted  
Missing second residue in struct_conn "C00489"  
Missing second residue in struct_conn "C00490"  
Missing second residue in struct_conn "C00491"  
Missing second residue in struct_conn "C00492"  
Missing second residue in struct_conn "C00493"  
1 messages similar to the above omitted  
Missing first residue in struct_conn "C00495"  
Missing first residue in struct_conn "C00496"  
Missing first residue in struct_conn "C00497"  
Missing first residue in struct_conn "C00498"  
Missing first residue in struct_conn "C00499"  
8 messages similar to the above omitted  
Missing second residue in struct_conn "C00508"  
Missing first residue in struct_conn "C00509"  
Missing first residue in struct_conn "C00510"  
Missing first residue in struct_conn "C00511"  
Missing first residue in struct_conn "C00512"  
Missing first residue in struct_conn "C00513"  
1 messages similar to the above omitted  
Missing second residue in struct_conn "C00515"  
Missing first residue in struct_conn "C00516"  
Missing first residue in struct_conn "C00517"  
Missing first residue in struct_conn "C00518"  
Missing first residue in struct_conn "C00519"  
Missing first residue in struct_conn "C00520"  
15 messages similar to the above omitted  
Missing second residue in struct_conn "C00536"  
Missing first residue in struct_conn "C00537"  
Missing first residue in struct_conn "C00538"  
Missing first residue in struct_conn "C00539"  
Missing first residue in struct_conn "C00540"  
Missing first residue in struct_conn "C00541"  
4 messages similar to the above omitted  
Missing second residue in struct_conn "C00546"  
Missing second residue in struct_conn "C00547"  
Missing first residue in struct_conn "C00548"  
Missing first residue in struct_conn "C00549"  
Missing first residue in struct_conn "C00550"  
Missing first residue in struct_conn "C00551"  
Missing first residue in struct_conn "C00552"  
Missing second residue in struct_conn "C00553"  
Missing second residue in struct_conn "C00554"  
Missing first residue in struct_conn "C00555"  
Missing first residue in struct_conn "C00556"  
Missing first residue in struct_conn "C00557"  
Missing first residue in struct_conn "C00558"  
Missing first residue in struct_conn "C00559"  
7 messages similar to the above omitted  
Missing second residue in struct_conn "C00567"  
Missing first residue in struct_conn "C00568"  
Missing first residue in struct_conn "C00569"  
Missing first residue in struct_conn "C00570"  
Missing first residue in struct_conn "C00571"  
Missing first residue in struct_conn "C00572"  
7 messages similar to the above omitted  
Missing second residue in struct_conn "C00580"  
Missing second residue in struct_conn "C00581"  
Missing first residue in struct_conn "C00582"  
Missing first residue in struct_conn "C00583"  
Missing first residue in struct_conn "C00584"  
Missing first residue in struct_conn "C00585"  
Missing first residue in struct_conn "C00586"  
41 messages similar to the above omitted  
Missing second residue in struct_conn "C00631"  
Missing second residue in struct_conn "C00632"  
Missing second residue in struct_conn "C00633"  
Missing second residue in struct_conn "C00634"  
Missing second residue in struct_conn "C00635"  
11 messages similar to the above omitted  
Missing first residue in struct_conn "C00650"  
Missing first residue in struct_conn "C00651"  
Missing first residue in struct_conn "C00652"  
Missing first residue in struct_conn "C00653"  
Missing first residue in struct_conn "C00654"  
33 messages similar to the above omitted  
Missing second residue in struct_conn "C00710"  
Missing second residue in struct_conn "C00711"  
Missing first residue in struct_conn "C00712"  
Missing first residue in struct_conn "C00713"  
Missing first residue in struct_conn "C00714"  
Missing first residue in struct_conn "C00715"  
Missing first residue in struct_conn "C00716"  
16 messages similar to the above omitted  
Bad residue range for struct_conf "1" near line 113  
Bad residue range for struct_conf "2" near line 114  
Bad residue range for struct_conf "3" near line 115  
Bad residue range for struct_conf "4" near line 116  
Bad residue range for struct_conf "5" near line 117  
16 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "A 2" near line 1230  
Invalid sheet range for struct_sheet_range "H 2" near line 1245  
Invalid sheet range for struct_sheet_range "I 4" near line 1249  
Invalid sheet range for struct_sheet_range "N 2" near line 1262  
Invalid sheet range for struct_sheet_range "U 2" near line 1277  
4 messages similar to the above omitted  
Atom H1 is not in the residue template for GLN #1 in chain C  
Atom H1 is not in the residue template for GLU #1 in chain D  
Atom H1 is not in the residue template for GLN #1 in chain C  
Atom H1 is not in the residue template for GLU #1 in chain D  
Atom H1 is not in the residue template for GLN #1 in chain C  
1 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 55083  
Skipping chem_comp category: Missing column 'type' near line 55247  
Skipping chem_comp category: Missing column 'type' near line 55411  
  
Chain information for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated-rsr24_real_space_refined.cif #1  
---  
Chain | Description  
A F K | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated-rsr24_real_space_refined.cif  
---  
Chain | Description  
1.2/A 1.2/F 1.2/K | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
  

> addh

Summary of feedback from adding hydrogens to 588AMS-
CH235p12-M5-293_apply_ncs_17.updated-coot-1.updated-
rsr24_real_space_refined.cif #1.2  
---  
notes | No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_17.updated-coot-1.updated-
rsr24_real_space_refined.cif (#1.2) chain A; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated-rsr24_real_space_refined.cif (#1.2) chain B; guessing termini
instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated-rsr24_real_space_refined.cif (#1.2) chain C; guessing termini
instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated-rsr24_real_space_refined.cif (#1.2) chain D; guessing termini
instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293_apply_ncs_17.updated-
coot-1.updated-rsr24_real_space_refined.cif (#1.2) chain F; guessing termini
instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A GLU 32, /B VAL 518, /C
GLN 1, /D GLU 1, /F GLU 32, /K GLU 32  
Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157,
/A GLY 312, /A ASN 409, /B GLY 572, /B GLY 572, /B GLY 572, /C GLY 134, /C GLY
134, /C GLY 134, /F THR 71, /F CYS 157, /F GLY 312, /F ASN 409, /K THR 71, /K
CYS 157, /K GLY 312, /K ASN 409  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A
ASN 147, /A ILE 309, /A ASN 398, /B ASP 664, /B SER 546, /B SER 546, /B SER
546, /C CYS 216, /C SER 128, /C SER 128, /C SER 128, /D GLY 212, /F VAL 503,
/F GLU 62, /F ASN 147, /F ILE 309, /F ASN 398, /K VAL 503, /K GLU 62, /K ASN
147, /K ILE 309, /K ASN 398  
2322 hydrogen bonds  
/A VAL 503 is not terminus, removing H atom from 'C'  
/A GLU 62 is not terminus, removing H atom from 'C'  
/A ASN 147 is not terminus, removing H atom from 'C'  
/A ILE 309 is not terminus, removing H atom from 'C'  
/A ASN 398 is not terminus, removing H atom from 'C'  
19 messages similar to the above omitted  
99 hydrogens added  
  

> open2 "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/cryosparc_P41_J32_009_volume_map_sharp_local.mrc"

Opened cryosparc_P41_J32_009_volume_map_sharp_local.mrc, grid size
320,320,320, pixel 1.07, shown at level 0.659, step 2, values float32  

> volume #2 step 1

> clipper associate #2 toModel #1

> clipper spotlight radius 32.00

> select #1

48027 atoms, 48519 bonds, 117 pseudobonds, 13 models selected  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 600, in __init__  
raise e  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1320, in __init__  
top, residue_templates = self.create_openmm_topology(atoms, template_dict)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 2718, in
create_openmm_topology  
atoms[i] = top.addAtom(aname, element,rmap[rid])  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/topology.py", line 190, in addAtom  
raise ValueError('All atoms within a residue must be contiguous')  
ValueError: All atoms within a residue must be contiguous  
  
ValueError: All atoms within a residue must be contiguous  
  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/topology.py", line 190, in addAtom  
raise ValueError('All atoms within a residue must be contiguous')  
  
See log for complete Python traceback.  
  

> select clear

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> hide atoms

> show cartoons

> select clear

No template found for residue A504 (NAG)  

Excluding residue  

No template found for residue A505 (NAG)  

Excluding residue  

No template found for residue A506 (BMA)  

Excluding residue  

No template found for residue A507 (MAN)  

Excluding residue  

No template found for residue A508 (MAN)  

Excluding residue  

No template found for residue A509 (MAN)  

Excluding residue  

No template found for residue A510 (MAN)  

Excluding residue  

No template found for residue A516 (NAG)  

Excluding residue  

No template found for residue A517 (NAG)  

Excluding residue  

No template found for residue A518 (BMA)  

Excluding residue  

No template found for residue A520 (NAG)  

Excluding residue  

No template found for residue A521 (NAG)  

Excluding residue  

No template found for residue A522 (NAG)  

Excluding residue  

No template found for residue A523 (NAG)  

Excluding residue  

No template found for residue A524 (NAG)  

Excluding residue  

No template found for residue A525 (BMA)  

Excluding residue  

No template found for residue A526 (NAG)  

Excluding residue  

No template found for residue A527 (NAG)  

Excluding residue  

No template found for residue A528 (NAG)  

Excluding residue  

No template found for residue A529 (NAG)  

Excluding residue  

No template found for residue B598 (CYS)  

Excluding residue  

No template found for residue B598 (CYS)  

Excluding residue  

No template found for residue B598 (CYS)  

Excluding residue  

No template found for residue B604 (CYS)  

Excluding residue  

No template found for residue B604 (CYS)  

Excluding residue  

No template found for residue B605 (CYS)  

Excluding residue  

No template found for residue B605 (CYS)  

Excluding residue  

No template found for residue C22 (CYS)  

Excluding residue  

No template found for residue C22 (CYS)  

Excluding residue  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 415
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 435
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0MB does not match the residue 442
(BMA)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0MA does not match the residue 444
(MAN)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0MA does not match the residue 444
(MAN)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0MA does not match the residue 444
(MAN)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0MA does not match the residue 444
(MAN)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 444
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 444
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0MB does not match the residue 444
(BMA)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 444
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 444
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 444
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 444
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 444
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0MB does not match the residue 444
(BMA)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 444
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 444
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 444
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 444
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYS does not match the residue 582 (THR)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYS does not match the residue 582 (THR)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYS does not match the residue 582 (THR)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYS does not match the residue 596 (TYR)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYS does not match the residue 596 (TYR)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYS does not match the residue 596 (TYR)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYS does not match the residue 596 (TYR)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYS does not match the residue 727 (SER)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYS does not match the residue 727 (SER)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__  
raise e  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem  
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
ignoreExternalBonds=ignoreExternalBonds)  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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 804 (CYS): CYM, CYX,
MC_CYF.  
  
Exception: Multiple matching templates found for residue 804 (CYS): CYM, CYX,
MC_CYF.  
  
File "/programs/x86_64-linux/chimerax/0.93/lib/python3.7/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: 3.3.0 NVIDIA 430.40
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: TYAN
Model: B7105F48TV8HR-2T-G
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 64 Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz
Cache Size: 22528 KB
Graphics:
	04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)
	Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]
	Kernel driver in use: ast

Change History (4)

comment:1 by Eric Pettersen, 5 years ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Template mismatch errors

comment:2 by Tristan Croll, 5 years ago

The good news is that I'm right on the verge of releasing a new version of ISOLDE that should make diagnosing and fixing problems like this much easier. I suspect the root cause is that your file does not have explicit LINKs for the glycans - neither ChimeraX nor ISOLDE currently attempt to detect and create these if they're not explicitly specified (likewise for disulfides - SSBOND records are needed).

in reply to: 3 ; follow-up: 3 comment:3 by kartik.manne@…, 5 years ago

Hi Tristan,

I have checked the glycans and SSbonds. They all seem to be linked.
However, I have previously worked with unlinked glycans by excluding them from the simulation and it worked.
Great to hear that you are releasing a newer version of ISOLDE which can fix these problems. When do you think it would be released? I can't wait to install the new version.

Best,
Kartik
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, August 4, 2020 12:08 PM
Cc: Kartik Manne, Ph.D. <kartik.manne@duke.edu>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #3592: Template mismatch errors

#3592: Template mismatch errors
-------------------------------------+---------------------------
          Reporter:  kartik.manne@…  |      Owner:  Tristan Croll
              Type:  defect          |     Status:  assigned
          Priority:  normal          |  Milestone:
         Component:  Third Party     |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+---------------------------

Comment (by Tristan Croll):

 The good news is that I'm right on the verge of releasing a new version of
 ISOLDE that should make diagnosing and fixing problems like this much
 easier. I suspect the root cause is that your file does not have explicit
 LINKs for the glycans - neither ChimeraX nor ISOLDE currently attempt to
 detect and create these if they're not explicitly specified (likewise for
 disulfides - SSBOND records are needed).

--
Ticket URL: <https://urldefense.com/v3/__https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3592*comment:2__;Iw!!OToaGQ!_NR61o3Gin_0mkIHau-mfxockH4goET9UBlUpkhPQjaaxEv7oLyAuIFUx3Y2hBSCECM$ >
ChimeraX <https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimerax/__;!!OToaGQ!_NR61o3Gin_0mkIHau-mfxockH4goET9UBlUpkhPQjaaxEv7oLyAuIFUx3Y2a6ySCfo$ >
ChimeraX Issue Tracker

comment:4 by Tristan Croll, 5 years ago

Resolution:	→ fixed
Status:	assigned → closed

Had a quick look at Kartik's coordinates. All of the issues in the model can be readily handled with the next ISOLDE release (tomorrow).

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