OpenMM runtime error: Release Object

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform: Linux-5.11.0-46-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX

open /home/cryosparc2/Documents/Rana/Lemon_del_H_38_coot_10.pdb format pdb

Chain information for Lemon_del_H_38_coot_10.pdb #1
---
Chain | Description
A | No description available
B | No description available
C E | No description available
D | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
g l | No description available
h j k m n | No description available
i | No description available
o | No description available
r | No description available

open /home/cryosparc2/Documents/Rana/State2ConsensusTrimmed.mrc

Opened State2ConsensusTrimmed.mrc as #2, grid size 140,140,200, pixel
1.62,1.62,1.62, shown at level 1.36, step 1, values float32

style stick

Changed 46163 atom styles

set bgColor white

select clear

[Repeated 1 time(s)]

select /O:255@CA

1 atom, 1 residue, 1 model selected

select up

5 atoms, 4 bonds, 1 residue, 1 model selected

select up

115 atoms, 114 bonds, 23 residues, 1 model selected

select up

1571 atoms, 1578 bonds, 311 residues, 1 model selected

isolde start sel

Expected fewer arguments

isolde start sel

Expected fewer arguments

isolde sim start sel

set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 146 residues in model #1 to IUPAC-IUB
standards.
Chain information for Lemon_del_H_38_coot_10.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/C 1.2/E | No description available
1.2/D | No description available
1.2/F | No description available
1.2/G | No description available
1.2/H | No description available
1.2/I | No description available
1.2/J | No description available
1.2/K | No description available
1.2/L | No description available
1.2/M | No description available
1.2/N | No description available
1.2/O | No description available
1.2/P | No description available
1.2/a | No description available
1.2/b | No description available
1.2/c | No description available
1.2/d | No description available
1.2/e | No description available
1.2/g 1.2/l | No description available
1.2/h 1.2/j 1.2/k 1.2/m 1.2/n | No description available
1.2/i | No description available
1.2/o | No description available
1.2/r | No description available

ISOLDE: stopped sim
Done loading forcefield

addh

Summary of feedback from adding hydrogens to Lemon_del_H_38_coot_10.pdb #1.2
---
warnings | Not adding hydrogens to /M ARG 28 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /M LYS 34 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /M LYS 35 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /M ASP 38 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /M GLN 43 CB because it is missing heavy-atom bond
partners
3518 messages similar to the above omitted
notes | No usable SEQRES records for Lemon_del_H_38_coot_10.pdb (#1.2) chain
A; guessing termini instead
No usable SEQRES records for Lemon_del_H_38_coot_10.pdb (#1.2) chain B;
guessing termini instead
No usable SEQRES records for Lemon_del_H_38_coot_10.pdb (#1.2) chain C;
guessing termini instead
No usable SEQRES records for Lemon_del_H_38_coot_10.pdb (#1.2) chain D;
guessing termini instead
No usable SEQRES records for Lemon_del_H_38_coot_10.pdb (#1.2) chain E;
guessing termini instead
26 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A TYR 21, /B LEU 15, /C TYR
21, /D GLU 12, /E TYR 21, /F GLU 12, /G GLN 12, /H LEU 14, /I MET 13, /J LEU
14, /K ASN 2, /L GLY 9, /M VAL 9, /N SER 12, /O ALA 2, /P ASP 2, /a PRO 23, /b
GLU 273, /c SER 11, /d ALA 6, /e ASN 32, /g GLU 8, /h GLU 8, /i GLU 8, /j GLU
8, /k GLU 8, /l GLU 8, /m GLU 8, /n GLU 8, /o ALA 9, /r VAL 332
Chain-initial residues that are not actual N termini: /A ILE 569, /B ASP 203,
/D ASP 199, /F GLY 200, /G HIS 178, /I LEU 172, /K PRO 176, /O LEU 181, /O THR
204, /O LEU 223, /P LEU 32, /P LYS 90, /P ILE 158, /a ASP 107, /a LYS 193, /a
HIS 710, /d THR 69, /d PRO 92, /d ARG 120, /d MET 147, /d LEU 247, /d GLY 284,
/e PRO 60
Chain-final residues that are actual C termini: /E ARG 623
Chain-final residues that are not actual C termini: /A GLU 619, /A VAL 558, /B
ARG 484, /B LYS 192, /C ARG 623, /D ARG 484, /D LYS 192, /F ARG 484, /F ARG
189, /G SER 226, /G VAL 166, /H ASN 110, /I SER 226, /I ILE 164, /J LYS 109,
/K SER 226, /K ASP 167, /L LYS 109, /M SER 221, /N ASN 118, /O GLY 339, /O LYS
171, /O PRO 189, /O ASP 218, /P ILE 327, /P PRO 17, /P MET 84, /P ARG 135, /a
ASP 819, /a SER 93, /a GLN 161, /a HIS 669, /b GLY 304, /c PRO 178, /d CYS
334, /d LEU 28, /d LEU 86, /d GLY 115, /d ILE 138, /d SER 242, /d SER 282, /e
GLU 68, /e ALA 56, /g GLN 160, /h ARG 162, /i ALA 163, /j ARG 162, /k ARG 162,
/l GLN 160, /m ARG 162, /n ARG 162, /o ALA 160, /r ILE 355
5473 hydrogen bonds
Adding 'H' to /A ILE 569
Adding 'H' to /B ASP 203
Adding 'H' to /D ASP 199
Adding 'H' to /F GLY 200
Adding 'H' to /G HIS 178
15 messages similar to the above omitted
/A GLU 619 is not terminus, removing H atom from 'C'
/B ARG 484 is not terminus, removing H atom from 'C'
/C ARG 623 is not terminus, removing H atom from 'C'
/D ARG 484 is not terminus, removing H atom from 'C'
/F ARG 484 is not terminus, removing H atom from 'C'
25 messages similar to the above omitted
36388 hydrogens added

ISOLDE: started sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
Opened State2ConsensusTrimmed.mrc as #1.1.1.1, grid size 140,140,200, pixel
1.62,1.62,1.62, shown at step 1, values float32
ISOLDE: started sim
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/home/cryosparc2/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/delayed_reaction.py", line 81, in callback
self.ff(*self.ff_args)
File "/home/cryosparc2/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1687, in
_update_coordinates_and_repeat
self.atoms.coords = th.coords
File "/home/cryosparc2/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 305, in coords
f(self._c_pointer, n, pointer(coords))
RuntimeError: Release Object

Error processing trigger "new frame":
RuntimeError: Release Object

File "/home/cryosparc2/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 305, in coords
f(self._c_pointer, n, pointer(coords))

See log for complete Python traceback.

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
ISOLDE: started sim
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/home/cryosparc2/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/delayed_reaction.py", line 81, in callback
self.ff(*self.ff_args)
File "/home/cryosparc2/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1687, in
_update_coordinates_and_repeat
self.atoms.coords = th.coords
File "/home/cryosparc2/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 305, in coords
f(self._c_pointer, n, pointer(coords))
RuntimeError: Release Object

Error processing trigger "new frame":
RuntimeError: Release Object

File "/home/cryosparc2/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 305, in coords
f(self._c_pointer, n, pointer(coords))

See log for complete Python traceback.

OpenGL version: 3.3.0 NVIDIA 470.86
OpenGL renderer: NVIDIA GeForce GTX 750 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
Cache Size: 15360 KB
Memory:

total used free shared buff/cache available

Mem: 31Gi 4.2Gi 19Gi 37Mi 7.4Gi 26Gi
Swap: 2.0Gi 0B 2.0Gi

Graphics:

03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107 GTX 750 Ti [10de:1380] (rev a2)
Subsystem: eVga.com. Corp. GM107 GTX 750 Ti [3842:3751]
Kernel driver in use: nvidia

Locale: ('en_CA', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:

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appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
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ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
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ChimeraX-FunctionKey: 1.0
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ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
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ChimeraX-IMOD: 1.0
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ChimeraX-ISOLDE: 1.3
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