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:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
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/604HC_CH235.12_M5-G458Y-293/RealSpaceRefine_18/604HC-
> CH235p12-M5-G458Y-293_apply_ncs_15.updated-
> rsr18_real_space_refined.updated.pdb"

Chain information for 604HC-CH235p12-M5-G458Y-293_apply_ncs_15.updated-
rsr18_real_space_refined.updated.pdb #1  
---  
Chain | Description  
A K | No description available  
A K | 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 | No description available  
  

> set bgColor white

> addh

Summary of feedback from adding hydrogens to 604HC-
CH235p12-M5-G458Y-293_apply_ncs_15.updated-
rsr18_real_space_refined.updated.pdb #1  
---  
notes | No usable SEQRES records for 604HC-
CH235p12-M5-G458Y-293_apply_ncs_15.updated-
rsr18_real_space_refined.updated.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for 604HC-CH235p12-M5-G458Y-293_apply_ncs_15.updated-
rsr18_real_space_refined.updated.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for 604HC-CH235p12-M5-G458Y-293_apply_ncs_15.updated-
rsr18_real_space_refined.updated.pdb (#1) chain B; guessing termini instead  
No usable SEQRES records for 604HC-CH235p12-M5-G458Y-293_apply_ncs_15.updated-
rsr18_real_space_refined.updated.pdb (#1) chain C; guessing termini instead  
No usable SEQRES records for 604HC-CH235p12-M5-G458Y-293_apply_ncs_15.updated-
rsr18_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 NAG 504, /B
VAL 518, /C GLN 1, /D GLU 1, /F NAG 520, /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, /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 BMA 518, /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, /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  
2564 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  
619 hydrogens added  
  

> open2 "/home/kartikmanne/Documents/CH235
> structures/604HC_CH235.12_M5-G458Y-293/cryosparc_P39_J45_007_volume_map_sharp_local.mrc"

Opened cryosparc_P39_J45_007_volume_map_sharp_local.mrc, grid size
320,320,320, pixel 1.07, shown at level 0.664, step 2, values float32  

> clipper associate #2 toModel #1

Chain information for 604HC-CH235p12-M5-G458Y-293_apply_ncs_15.updated-
rsr18_real_space_refined.updated.pdb  
---  
Chain | Description  
1.2/A 1.2/K | No description available  
1.2/A 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  
1.2/F | No description available  
1.2/F | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> clipper spotlight radius 52.00

QWidget::repaint: Recursive repaint detected  

> select #1

48651 atoms, 49171 bonds, 68 pseudobonds, 13 models selected  

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 467
(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 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 467 (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 467 (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

[Eric Pettersen]

Possibly closable as a duplicate

[Tristan Croll]

That's a rather odd error. It's saying the auto-assigned template (0YB, corresponding to a terminal NAG with no further pendant sugars) is wrong... but then when it falls back to looking for matches by topology, it finds multiple matching templates *including* 0YB. Almost certainly something's wrong with that sugar, but I'm at a loss to say what. Any chance you could send me a copy of the model so I can take a closer look?