Problem matching GLYCAM templates

[kartik.manne@…]

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/RealSpaceRefine_9/588AMS-
> CH235p12-M5-293-placed_model.updated-rsr9_real_space_refined.updated.pdb"

Chain information for 588AMS-CH235p12-M5-293-placed_model.updated-
rsr9_real_space_refined.updated.pdb #1  
---  
Chain | Description  
A F 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 K | No description available  
  

> set bgColor white

> addh

Summary of feedback from adding hydrogens to 588AMS-
CH235p12-M5-293-placed_model.updated-rsr9_real_space_refined.updated.pdb #1  
---  
warnings | Unknown hybridization for atom (O4) of residue type NAG; not adding
hydrogens to it  
Unknown hybridization for atom (O3) of residue type BMA; not adding hydrogens
to it  
Unknown hybridization for atom (O3) of residue type MAN; not adding hydrogens
to it  
notes | No usable SEQRES records for 588AMS-
CH235p12-M5-293-placed_model.updated-rsr9_real_space_refined.updated.pdb (#1)
chain A; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293-placed_model.updated-
rsr9_real_space_refined.updated.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293-placed_model.updated-
rsr9_real_space_refined.updated.pdb (#1) chain B; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293-placed_model.updated-
rsr9_real_space_refined.updated.pdb (#1) chain C; guessing termini instead  
No usable SEQRES records for 588AMS-CH235p12-M5-293-placed_model.updated-
rsr9_real_space_refined.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 522, /A MAN 510, /B
VAL 518, /C GLN 1, /D GLU 1, /F NAG 522, /F NAG 504, /G VAL 518, /H GLN 1, /I
GLU 1, /K NAG 522, /K NAG 504, /L VAL 518, /M GLN 1, /N GLU 1  
Chain-initial residues that are not actual N termini: /A CYS 157, /A GLY 312,
/A ASN 409, /A NAG 520, /C GLY 134, /F CYS 157, /F GLY 312, /F ASN 409, /F NAG
520, /H GLY 134, /K CYS 157, /K GLY 312, /K ASN 409, /K NAG 520, /M GLY 134  
Chain-final residues that are actual C termini: /A NAG 521, /F NAG 521, /K NAG
521  
Chain-final residues that are not actual C termini: /A VAL 503, /A ASN 147, /A
ILE 309, /A ASN 398, /A BMA 518, /B ASP 664, /C CYS 216, /C SER 128, /D GLY
212, /F VAL 503, /F ASN 147, /F ILE 309, /F ASN 398, /F BMA 518, /G ASP 664,
/H CYS 216, /H SER 128, /I GLY 212, /K VAL 503, /K ASN 147, /K ILE 309, /K ASN
398, /K BMA 518, /L ASP 664, /M CYS 216, /M SER 128, /N GLY 212  
2572 hydrogen bonds  
/A VAL 503 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'  
/B ASP 664 is not terminus, removing H atom from 'C'  
19 messages similar to the above omitted  
348 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  

> clipper associate #2 toModel #1

Chain information for 588AMS-CH235p12-M5-293-placed_model.updated-
rsr9_real_space_refined.updated.pdb  
---  
Chain | Description  
1.2/A 1.2/F 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 1.2/K | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> clipper spotlight radius 52.00

QWidget::repaint: Recursive repaint detected  

> select #1

48646 atoms, 49169 bonds, 64 pseudobonds, 13 models selected  

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 A508 (MAN)  

Excluding residue  

No template found for residue A519 (NAG)  

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 452
(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_4YB does not match the residue 452
(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_3MB does not match the residue 452
(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_3MA does not match the residue 453
(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 463
(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/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 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 463 (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 463 (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 463 (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 463 (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.  
  




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

[Tristan Croll]

Addressing in #3538