sm.start_sim: _openmm.new_Context: bad allocation

[352884536@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:\dopamine receptors project\data processing\D5R_Complex-coot-0.pdb"
> format pdb

Summary of feedback from opening D:\dopamine receptors project\data
processing\D5R_Complex-coot-0.pdb  
---  
warning | Ignored bad PDB record found on line 8027  
END  
  
Chain information for D5R_Complex-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
E | No description available  
  

> open "D:/dopamine receptors project/data
> processing/P41_pJ90_dehz_flipped_2d6A.mrc"

Opened P41_pJ90_dehz_flipped_2d6A.mrc, grid size 300,300,300, pixel 0.73,
shown at level 0.0187, step 2, values float32  

> volume #2 step 1

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for D5R_Complex-coot-0.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/E | No description available  
  
Done loading forcefield  

> set bgColor white

> addh

Summary of feedback from adding hydrogens to D5R_Complex-coot-0.pdb #1.2  
---  
notes | No usable SEQRES records for D5R_Complex-coot-0.pdb (#1.2) chain A;
guessing termini instead  
No usable SEQRES records for D5R_Complex-coot-0.pdb (#1.2) chain B; guessing
termini instead  
No usable SEQRES records for D5R_Complex-coot-0.pdb (#1.2) chain C; guessing
termini instead  
No usable SEQRES records for D5R_Complex-coot-0.pdb (#1.2) chain E; guessing
termini instead  
Chain-initial residues that are actual N termini: /A SER 6, /B ALA 33, /C GLN
3, /E THR 8  
Chain-initial residues that are not actual N termini: /B LEU 221, /B LYS 293,
/B PRO 334, /E THR 203, /E ASN 260  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A TRP 343, /B ALA 370, /B
LEU 178, /B HIS 268, /B GLY 324, /C PHE 61, /E LEU 392, /E ILE 61, /E SER 251  
775 hydrogen bonds  
Adding 'H' to /B LEU 221  
Adding 'H' to /B LYS 293  
Adding 'H' to /E THR 203  
Adding 'H' to /E ASN 260  
/A TRP 343 is not terminus, removing H atom from 'C'  
/B ALA 370 is not terminus, removing H atom from 'C'  
/B LEU 178 is not terminus, removing H atom from 'C'  
/B HIS 268 is not terminus, removing H atom from 'C'  
/B GLY 324 is not terminus, removing H atom from 'C'  
4 messages similar to the above omitted  
7980 hydrogens added  
  

> clipper associate #1 toModel #2

Invalid "toModel" argument: Must specify 1 structure, got 0 for "#2"  

> clipper associate #2 toModel #1

> clipper spotlight radius 120.00

> isolde start

Chain C, residue 5 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 6 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 7 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 8 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 9 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 10 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 11 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 12 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 13 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 14 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 15 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 16 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 17 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 18 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 19 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 20 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 21 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 22 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 23 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 24 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 25 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 26 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 27 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 28 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 29 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 30 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 31 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 32 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 33 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 34 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 35 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 36 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 37 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 38 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 39 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 40 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 41 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 42 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 43 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 44 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 45 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 46 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 47 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 48 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 49 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 50 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 51 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 52 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 53 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 54 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 55 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 56 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 57 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 58 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 59 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 61 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 5 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 6 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 7 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 8 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 9 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 10 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 11 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 12 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 13 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 14 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 15 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 16 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 17 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 18 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 19 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 20 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 21 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 22 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 23 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 24 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 25 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 26 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 27 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 28 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 29 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 30 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 31 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 32 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 33 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 34 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 35 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 36 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 37 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 38 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 39 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 40 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 41 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 42 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 43 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 44 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 45 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 46 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 47 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 48 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 49 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 50 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 51 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 52 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 53 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 54 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 55 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 56 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 57 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 58 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 59 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 61 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 5 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 30 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 33 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 34 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 35 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 36 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 37 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 38 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 39 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 40 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 41 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 42 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 45 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 46 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 47 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 48 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 49 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 50 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 51 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 52 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 53 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 54 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 55 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 56 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 57 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 58 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 59 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 61 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Traceback (most recent call last):  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 2735, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 2774, in start_sim  
sm.start_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 670, in start_sim  
sh.start_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1597, in start_sim  
self._prepare_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1558, in
_prepare_sim  
integrator, platform, properties)  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\simtk\openmm\app\simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6270, in __init__  
this = _openmm.new_Context(*args)  
Exception: bad allocation  
  
Exception: bad allocation  
  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6270, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  

Chain C, residue 5 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 6 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 11 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 14 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 15 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 18 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 19 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 22 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 25 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 27 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 28 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 29 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 30 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 31 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 32 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 33 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 34 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 35 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 36 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 37 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 38 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 39 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 40 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 41 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 42 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 43 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 44 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 45 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 46 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 47 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 48 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 49 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 50 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 51 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 52 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 53 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 54 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 55 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 56 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 57 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 58 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 59 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 61 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 5 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 6 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 7 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 8 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 9 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 10 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 11 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 12 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 13 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 14 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 15 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 16 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 17 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 18 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 19 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 20 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 21 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 22 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 23 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 24 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 25 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 26 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 27 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 28 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 29 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 30 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 31 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 32 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 33 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 34 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 35 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 36 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 37 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 38 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 39 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 40 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 41 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 42 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 43 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 44 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 45 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 46 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 47 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 48 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 49 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 50 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 51 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 52 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 53 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 54 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 55 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 56 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 57 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 58 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 59 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 60 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Chain C, residue 61 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> delete pseudobonds

Traceback (most recent call last):  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 2735, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 2774, in start_sim  
sm.start_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 670, in start_sim  
sh.start_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1597, in start_sim  
self._prepare_sim()  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1558, in
_prepare_sim  
integrator, platform, properties)  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\simtk\openmm\app\simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6270, in __init__  
this = _openmm.new_Context(*args)  
Exception: bad allocation  
  
Exception: bad allocation  
  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6270, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1161, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1954, in
update_dihedral_restraints  
restraints.enableds, restraints.spring_constants, restraints.targets,
restraints.cutoffs)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\chimeraX\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1227, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2430, in
update_tuggables  
tuggables.enableds, tuggables.spring_constants, tuggables.targets/10)  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File "C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1217, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 516.94
OpenGL renderer: NVIDIA GeForce GTX 1650 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: IPASON
Model:  
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 17,130,639,360
MaxProcessMemory: 137,438,953,344
CPU: 6 AMD Ryzen 5 3500X 6-Core Processor             "
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Eric Pettersen]

Version 1.0

[Tristan Croll]

My first (and most important) piece of advice is to update to ChimeraX 1.5 and the associated version of ISOLDE (also 1.5). ISOLDE 1.0 is almost 2 and a half years back - there have been so many changes and improvements since then that it's almost a completely different program. The first thing I notice from the log is that your model seems to have more than one chain C - a dangerous practice in general, although ISOLDE should be able to handle it these days. I'd strongly recommend fixing that in any case. Beyond that, please try re-running your scenario in the latest ISOLDE and let me know if it still doesn't work.