Opened 12 months ago

Closed 12 months ago

#16243 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-14.7-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000000031f226000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031e223000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031d220000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031c21d000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031b21a000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031a217000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000319214000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000318211000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031720e000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031620b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000315208000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000314205000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000313202000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003121ff000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003111fc000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000200216240 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.chem_group._chem_group, chimerax.atom_search.ast, chimerax.coulombic._esp (total: 65)


{"app_name":"ChimeraX","timestamp":"2024-11-04 09:49:17.00 +0100","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.7 (23H124)","roots_installed":0,"name":"ChimeraX","incident_id":"A0D576B8-FCAD-42A4-9248-8DD30CC9B986"}
{
  "uptime" : 630000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 1760076204,
  "deployVersion" : 210,
  "modelCode" : "Mac15,6",
  "coalitionID" : 98386,
  "osVersion" : {
    "train" : "macOS 14.7",
    "build" : "23H124",
    "releaseType" : "User"
  },
  "captureTime" : "2024-11-04 09:48:34.7105 +0100",
  "codeSigningMonitor" : 1,
  "incident" : "A0D576B8-FCAD-42A4-9248-8DD30CC9B986",
  "pid" : 90110,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-10-15 16:38:13.9569 +0200",
  "procStartAbsTime" : 8257205897342,
  "procExitAbsTime" : 15256638329101,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"5E8A07C1-54C7-517C-B699-7A410F38BFA4","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "CF866F4B-9D1F-AECA-8792-54A1D2B1A0D2",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "wakeTime" : 3,
  "sleepWakeUUID" : "CA06DE45-CE0A-47C6-9176-43674BAB7AB9",
  "sip" : "enabled",
  "vmRegionInfo" : "0x3cd70caf09a8 is not in any region.  Bytes after previous region: 66413292095913  Bytes before following region: 38658787833432\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x00003cd70caf09a8","rawCodes":[1,66894328433064],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00003cd70caf09a8"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":90110},
  "vmregioninfo" : "0x3cd70caf09a8 is not in any region.  Bytes after previous region: 66413292095913  Bytes before following region: 38658787833432\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/u0154680/Documents/DailyWork/ChimeraX_Big_Structure_Overlay_241014.cxs

opened ChimeraX session  

> hide #19 models

> hide #20 models

> hide #26 models

> close #22-26

> open
> /Volumes/gbw_lvs/GBW-0009_VIB_DS_Images/Carlos_L/Projects/GSEC/In_Silico/Structure/Chai-
> lab/PF_878501/num_diffn_timesteps_1000/pred.model_idx_0.cif
> /Volumes/gbw_lvs/GBW-0009_VIB_DS_Images/Carlos_L/Projects/GSEC/In_Silico/Structure/Chai-
> lab/PF_878501/num_diffn_timesteps_1000/pred.model_idx_1.cif
> /Volumes/gbw_lvs/GBW-0009_VIB_DS_Images/Carlos_L/Projects/GSEC/In_Silico/Structure/Chai-
> lab/PF_878501/num_diffn_timesteps_1000/pred.model_idx_2.cif
> /Volumes/gbw_lvs/GBW-0009_VIB_DS_Images/Carlos_L/Projects/GSEC/In_Silico/Structure/Chai-
> lab/PF_878501/num_diffn_timesteps_1000/pred.model_idx_3.cif
> /Volumes/gbw_lvs/GBW-0009_VIB_DS_Images/Carlos_L/Projects/GSEC/In_Silico/Structure/Chai-
> lab/PF_878501/num_diffn_timesteps_1000/pred.model_idx_4.cif

Summary of feedback from opening
/Volumes/gbw_lvs/GBW-0009_VIB_DS_Images/Carlos_L/Projects/GSEC/In_Silico/Structure/Chai-
lab/PF_878501/num_diffn_timesteps_1000/pred.model_idx_0.cif  
---  
warning | Atom C_1 is not in the residue template for LIG /F:1  
  
Summary of feedback from opening
/Volumes/gbw_lvs/GBW-0009_VIB_DS_Images/Carlos_L/Projects/GSEC/In_Silico/Structure/Chai-
lab/PF_878501/num_diffn_timesteps_1000/pred.model_idx_1.cif  
---  
warning | Atom C_1 is not in the residue template for LIG /F:1  
  
Summary of feedback from opening
/Volumes/gbw_lvs/GBW-0009_VIB_DS_Images/Carlos_L/Projects/GSEC/In_Silico/Structure/Chai-
lab/PF_878501/num_diffn_timesteps_1000/pred.model_idx_2.cif  
---  
warning | Atom C_1 is not in the residue template for LIG /F:1  
  
Summary of feedback from opening
/Volumes/gbw_lvs/GBW-0009_VIB_DS_Images/Carlos_L/Projects/GSEC/In_Silico/Structure/Chai-
lab/PF_878501/num_diffn_timesteps_1000/pred.model_idx_3.cif  
---  
warning | Atom C_1 is not in the residue template for LIG /F:1  
  
Summary of feedback from opening
/Volumes/gbw_lvs/GBW-0009_VIB_DS_Images/Carlos_L/Projects/GSEC/In_Silico/Structure/Chai-
lab/PF_878501/num_diffn_timesteps_1000/pred.model_idx_4.cif  
---  
warning | Atom C_1 is not in the residue template for LIG /F:1  
  
pred.model_idx_0.cif title:  
Chai-1 predicted structure [more info...]  
  
Chain information for pred.model_idx_0.cif #22  
---  
Chain | Description  
A | Domain1  
B | Domain2  
C | Domain3  
D | Domain4  
E | Abeta46  
  
Non-standard residues in pred.model_idx_0.cif #22  
---  
LIG — (LIG)  
  
Color pred.model_idx_0.cif by residue attribute pLDDT_score  
pred.model_idx_1.cif title:  
Chai-1 predicted structure [more info...]  
  
Chain information for pred.model_idx_1.cif #23  
---  
Chain | Description  
A | Domain1  
B | Domain2  
C | Domain3  
D | Domain4  
E | Abeta46  
  
Non-standard residues in pred.model_idx_1.cif #23  
---  
LIG — (LIG)  
  
Color pred.model_idx_1.cif by residue attribute pLDDT_score  
pred.model_idx_2.cif title:  
Chai-1 predicted structure [more info...]  
  
Chain information for pred.model_idx_2.cif #24  
---  
Chain | Description  
A | Domain1  
B | Domain2  
C | Domain3  
D | Domain4  
E | Abeta46  
  
Non-standard residues in pred.model_idx_2.cif #24  
---  
LIG — (LIG)  
  
Color pred.model_idx_2.cif by residue attribute pLDDT_score  
pred.model_idx_3.cif title:  
Chai-1 predicted structure [more info...]  
  
Chain information for pred.model_idx_3.cif #25  
---  
Chain | Description  
A | Domain1  
B | Domain2  
C | Domain3  
D | Domain4  
E | Abeta46  
  
Non-standard residues in pred.model_idx_3.cif #25  
---  
LIG — (LIG)  
  
Color pred.model_idx_3.cif by residue attribute pLDDT_score  
pred.model_idx_4.cif title:  
Chai-1 predicted structure [more info...]  
  
Chain information for pred.model_idx_4.cif #26  
---  
Chain | Description  
A | Domain1  
B | Domain2  
C | Domain3  
D | Domain4  
E | Abeta46  
  
Non-standard residues in pred.model_idx_4.cif #26  
---  
LIG — (LIG)  
  
Color pred.model_idx_4.cif by residue attribute pLDDT_score  

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #22-26 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RSR57.pdb, chain B (#1) with pred.model_idx_0.cif, chain B (#22),
sequence alignment score = 1534.9  
RMSD between 250 pruned atom pairs is 1.036 angstroms; (across all 309 pairs:
2.446)  
  
Matchmaker RSR57.pdb, chain B (#1) with pred.model_idx_1.cif, chain B (#23),
sequence alignment score = 1542.7  
RMSD between 263 pruned atom pairs is 0.987 angstroms; (across all 309 pairs:
2.072)  
  
Matchmaker RSR57.pdb, chain B (#1) with pred.model_idx_2.cif, chain B (#24),
sequence alignment score = 1557.1  
RMSD between 247 pruned atom pairs is 1.021 angstroms; (across all 309 pairs:
2.639)  
  
Matchmaker RSR57.pdb, chain B (#1) with pred.model_idx_3.cif, chain B (#25),
sequence alignment score = 1557.1  
RMSD between 239 pruned atom pairs is 1.031 angstroms; (across all 309 pairs:
2.388)  
  
Matchmaker RSR57.pdb, chain B (#1) with pred.model_idx_4.cif, chain B (#26),
sequence alignment score = 1543.9  
RMSD between 257 pruned atom pairs is 0.981 angstroms; (across all 309 pairs:
2.354)  
  

> style #22-26#!1 stick

Changed 74629 atom styles  

> show #22-26#!1 cartoons

> select ::name="GI9"

112 atoms, 120 bonds, 2 residues, 2 models selected  

> ui tool show "Color Actions"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color sel lime

> hide #26 models

> hide #25 models

> hide #24 models

> hide #23 models

> hide #22 models

> hide #!1 models

> show #!1 models

> show #!1 atoms

> select clear

> select ::name="GI9"

112 atoms, 120 bonds, 2 residues, 2 models selected  

> show #!1 atoms

> show #!1 target ab

> show #!21 models

> hide #!1 models

> color sel byhetero

> select clear

> show #!1 models

> hide #21.1 models

> show #21.1 models

> hide #21.1 models

> hide #!21 models

> show #!21 models

> select ::name="GI9"

112 atoms, 120 bonds, 2 residues, 2 models selected  

> select ~sel & ##selected

42128 atoms, 42676 bonds, 22 pseudobonds, 2664 residues, 5 models selected  

> hide sel & #!21 atoms

> hide sel & #!21 cartoons

> hide sel & #!21 surfaces

> show #22 models

> select ::name="LIG"

170 atoms, 190 bonds, 5 residues, 5 models selected  

> show #23 models

> show #24 models

> show #25 models

> show #26 models

> color sel orange red

> color sel byhetero

> select clear

> hide #!1 models

> show #!1 models

> save
> /Volumes/gbw_lvs/GBW-0009_VIB_DS_Images/Carlos_L/Projects/GSEC/In_Silico/Structure/Chai-
> lab/PF_878501/num_diffn_timesteps_1000/AF3_vs_Chai_RSR57_GI9_complex_07.png
> width 1346 height 850 supersample 3

> hide #26 models

> hide #25 models

> hide #24 models

> hide #23 models

> hide #22 models

> show #22 models

> show #23 models

> show #24 models

> show #25 models

> show #26 models

> hide #26 models

> hide #25 models

> hide #24 models

> hide #23 models

> hide #22 models

> show #22 models

> show #23 models

> show #24 models

> show #25 models

> show #26 models

> open
> /Users/u0154680/Downloads/fold_gsec_complex_af3_2024_08_27_11_14/fold_gsec_complex_af3_2024_08_27_11_14_model_4.cif
> /Users/u0154680/Downloads/fold_gsec_complex_af3_2024_08_27_11_14/fold_gsec_complex_af3_2024_08_27_11_14_model_3.cif
> /Users/u0154680/Downloads/fold_gsec_complex_af3_2024_08_27_11_14/fold_gsec_complex_af3_2024_08_27_11_14_model_2.cif
> /Users/u0154680/Downloads/fold_gsec_complex_af3_2024_08_27_11_14/fold_gsec_complex_af3_2024_08_27_11_14_model_1.cif
> /Users/u0154680/Downloads/fold_gsec_complex_af3_2024_08_27_11_14/fold_gsec_complex_af3_2024_08_27_11_14_model_0.cif

Chain information for fold_gsec_complex_af3_2024_08_27_11_14_model_4.cif #27  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_gsec_complex_af3_2024_08_27_11_14_model_3.cif #28  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_gsec_complex_af3_2024_08_27_11_14_model_2.cif #29  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_gsec_complex_af3_2024_08_27_11_14_model_1.cif #30  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_gsec_complex_af3_2024_08_27_11_14_model_0.cif #31  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> hide #!21 models

> hide #22 models

> hide #23 models

> hide #24 models

> hide #25 models

> hide #26 models

> hide #!1 models

> show #!1 models

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #27-31 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RSR57.pdb, chain B (#1) with
fold_gsec_complex_af3_2024_08_27_11_14_model_4.cif, chain B (#27), sequence
alignment score = 1536.7  
RMSD between 287 pruned atom pairs is 0.763 angstroms; (across all 309 pairs:
1.073)  
  
Matchmaker RSR57.pdb, chain B (#1) with
fold_gsec_complex_af3_2024_08_27_11_14_model_3.cif, chain B (#28), sequence
alignment score = 1548.7  
RMSD between 286 pruned atom pairs is 0.768 angstroms; (across all 309 pairs:
1.100)  
  
Matchmaker RSR57.pdb, chain B (#1) with
fold_gsec_complex_af3_2024_08_27_11_14_model_2.cif, chain B (#29), sequence
alignment score = 1548.1  
RMSD between 293 pruned atom pairs is 0.788 angstroms; (across all 309 pairs:
1.081)  
  
Matchmaker RSR57.pdb, chain B (#1) with
fold_gsec_complex_af3_2024_08_27_11_14_model_1.cif, chain B (#30), sequence
alignment score = 1551.1  
RMSD between 287 pruned atom pairs is 0.754 angstroms; (across all 309 pairs:
1.146)  
  
Matchmaker RSR57.pdb, chain B (#1) with
fold_gsec_complex_af3_2024_08_27_11_14_model_0.cif, chain B (#31), sequence
alignment score = 1554.1  
RMSD between 288 pruned atom pairs is 0.788 angstroms; (across all 309 pairs:
1.140)  
  

> style #27-31#!1 stick

Changed 74569 atom styles  

> show #27-31#!1 cartoons

> hide #!1 models

> show #!1 models

> ui tool show "Color Actions"

> color forest green

> undo

> select add #1

20874 atoms, 21150 bonds, 2 pseudobonds, 1314 residues, 2 models selected  

> color sel forest green target a

> color sel byhetero target a

> color sel bychain target a

> color sel bypolymer target a

> hide #27 models

> hide #28 models

> hide #29 models

> hide #30 models

> hide #31 models

> select clear

> show #27 models

> hide #27 models

> show #27 models

> hide #27 models

> show #27 models

> hide #27 models

> select add #1

20874 atoms, 21150 bonds, 2 pseudobonds, 1314 residues, 2 models selected  

> color sel light sea green target a

> color sel forest green target a

> color sel lime target a

> color sel forest green target a

> select clear

> show #27 models

> show #29 models

> show #30 models

> show #31 models

> show #28 models

> show #19 models

> hide #19 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> select ::name="LIG"

170 atoms, 190 bonds, 5 residues, 5 models selected  

> select ::name="GI9"

112 atoms, 120 bonds, 2 residues, 2 models selected  

> select ~sel & ##selected

42128 atoms, 42676 bonds, 22 pseudobonds, 2664 residues, 5 models selected  

> hide sel & #!18 cartoons

> hide sel & #!18 atoms

> save /Users/u0154680/Documents/DailyWork/AF3_5models_vs_RSR57_01.png width
> 1346 height 850 supersample 3

> lighting simple

> lighting soft

> lighting full

> lighting flat

> graphics silhouettes false

> lighting shadows true intensity 0.5

> lighting simple

> lighting shadows true

> lighting soft

> lighting simple

> save /Users/u0154680/Documents/DailyWork/AF3_5models_vs_RSR57_02.png width
> 1346 height 850 supersample 3

> select ::name="GI9"

112 atoms, 120 bonds, 2 residues, 2 models selected  

> select ::name="GI9"

112 atoms, 120 bonds, 2 residues, 2 models selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select sel : select ~sel

327242 atoms, 333955 bonds, 29 pseudobonds, 33256 residues, 40 models selected  

> hide sel & #27-31#!1,18 atoms

> hide sel & #27-31#!1,18 cartoons

> hide #27 models

> hide #28 models

> hide #29 models

> hide #30 models

> hide #31 models

> show #26 models

> show #25 models

> show #24 models

> show #23 models

> show #22 models

> hide sel & #22-26#!1,18 atoms

> hide sel & #22-26#!1,18 cartoons

> hide #!1 models

> hide #!18 models

> show #!18 models

> show #!1 models

> hide #26 models

> hide #25 models

> hide #24 models

> hide #23 models

> hide #22 models

> show #27 models

> show #!16 models

> hide #27 models

> show #27 models

> hide #!16 models

> show #!15 models

> show #!14 models

> hide #!14 models

> hide #!15 models

> show #28 models

> show #29 models

> show #30 models

> show #31 models

> hide #27 models

> hide #28 models

> hide #29 models

> hide #30 models

> hide #31 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hide #!1 models

> hide #!18 models

> show #10 models

> select add #10

327274 atoms, 333991 bonds, 29 pseudobonds, 33257 residues, 46 models selected  

> select clear

> select add #10

32 atoms, 36 bonds, 1 residue, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge -21) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmplg8i563b/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmplg8i563b/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmplg8i563b/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Charges failed to converge using fast method; re-running using slower more
stable method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmplg8i563b/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmplg8i563b/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmplg8i563b/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
  
Contents of sqm.out:

    
    
                --------------------------------------------------------
                                 AMBER SQM VERSION 19
     
                                         By
                  Ross C. Walker, Michael F. Crowley, Scott Brozell,
                             Tim Giese, Andreas W. Goetz,
                            Tai-Sung Lee and David A. Case
     
                --------------------------------------------------------
     
    
    --------------------------------------------------------------------------------
      QM CALCULATION INFO
    --------------------------------------------------------------------------------
    
    | QMMM: Citation for AMBER QMMM Run:
    | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
    
    QMMM: SINGLET STATE CALCULATION
    QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 83
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: F : M.J.S.DEWAR et al. THEOCHEM, 180, 1, (1988)
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    
    | QMMM: *** SCF convergence criteria ***
    | QMMM: Energy change                :  0.1D-09 kcal/mol
    | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    | QMMM: Density matrix change        :  0.5D-06
    | QMMM: Maximum number of SCF cycles :     1000
    
    | QMMM: *** Diagonalization Routine Information ***
    | QMMM: Pseudo diagonalizations are allowed.
    | QMMM: Auto diagonalization routine selection is in use.
    | QMMM:
    | QMMM: Timing diagonalization routines:
    | QMMM:                              norbs =      125
    | QMMM:    diag iterations used for timing =       10
    | QMMM:
    | QMMM:              Internal diag routine = 0.018856 seconds
    | QMMM:                 Dspev diag routine = 0.018480 seconds
    | QMMM:                Dspevd diag routine = 0.014596 seconds
    | QMMM:                Dspevx diag routine = 0.065912 seconds
    | QMMM:                 Dsyev diag routine = 0.019633 seconds
    | QMMM:                Dsyevd diag routine = 0.015744 seconds
    | QMMM:                Dsyevr diag routine = 0.016902 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.006109 seconds
    | QMMM:
    | QMMM: Using dspevd routine (diag_routine=3).
    
      QMMM: QM Region Cartesian Coordinates (*=link atom) 
      QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
      QMMM:     1        1      F      135.1190  107.8430  114.2820
      QMMM:     2        2      C      135.7000  108.9610  114.8430
      QMMM:     3        3      F      137.0630  108.8740  114.6380
      QMMM:     4        4      F      135.1540  110.0650  114.2240
      QMMM:     5        5      C      135.4660  108.9930  116.3440
      QMMM:     6        6      O      135.9880  107.9030  116.9990
      QMMM:     7        7      C      136.0230  107.6690  118.3640
      QMMM:     8        8      C      135.4750  108.6210  119.2960
      QMMM:     9        9      N      134.8960  109.7790  119.0770
      QMMM:    10       10      C      134.5490  110.3100  120.3070
      QMMM:    11       11      N      134.9150  109.4830  121.2580
      QMMM:    12       12      N      135.5000  108.4100  120.6520
      QMMM:    13       13      C      136.0760  107.2310  121.1150
      QMMM:    14       14      C      136.6080  106.3050  120.2550
      QMMM:    15       15      C      136.5920  106.5110  118.8280
      QMMM:    16       16      N      133.8980  111.5570  120.5090
      QMMM:    17       17      C      133.0430  112.2050  119.4990
      QMMM:    18       18      C      133.0670  113.7120  119.6060
      QMMM:    19       19      C      132.2400  114.4550  118.5650
      QMMM:    20       20      N      130.8720  113.9120  118.5270
      QMMM:    21       21      C      129.7720  114.8150  118.3380
      QMMM:    22       22      O      129.6090  115.6060  117.2740
      QMMM:    23       23      C      128.4830  116.2860  117.4740
      QMMM:    24       24      N      127.9570  115.9310  118.6230
      QMMM:    25       25      N      128.7760  114.9930  119.1770
      QMMM:    26       26      C      127.9090  117.3130  116.5130
      QMMM:    27       27      C      130.6340  112.4710  118.6910
      QMMM:    28       28      C      131.5750  111.9900  119.7850
      QMMM:    29       29      C      131.4650  112.7430  121.0950
      QMMM:    30       30      C      132.3660  113.9530  120.9260
      QMMM:    31       31      C      136.2380  110.2240  116.8460
      QMMM:    32       32      H      134.0270  112.0200  121.3860
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10    12826.8179 kcal/mol       51.1855 kcal/(mol*A)
    xmin    20    11664.3619 kcal/mol       36.4741 kcal/(mol*A)
    xmin    30    10764.5606 kcal/mol       40.6614 kcal/(mol*A)
    xmin    40     9962.7702 kcal/mol       25.8247 kcal/(mol*A)
    xmin    50     9275.0322 kcal/mol       18.6148 kcal/(mol*A)
    xmin    60     8822.9371 kcal/mol       14.9385 kcal/(mol*A)
    
    QMMM: ERROR!
    QMMM: Unable to achieve self consistency to the tolerances specified
    QMMM: No convergence in SCF after   1000 steps.
    QMMM: E =  -0.6485E+06 DeltaE =  -0.2844E+03 DeltaP =   0.1144E+01
    QMMM: Smallest DeltaE =  -0.1164E-09 DeltaP =   0.3721E-07 Step =      3
    
    

  
Failure running ANTECHAMBER for residue UNL Check reply log for details  

> mlp sel

mlp: no amino acids specified  

> style sel sphere

Changed 32 atom styles  

> show sel surfaces

> style sel stick

Changed 32 atom styles  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge -21) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpnb10zed6/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpnb10zed6/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpnb10zed6/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Charges failed to converge using fast method; re-running using slower more
stable method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpnb10zed6/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpnb10zed6/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpnb10zed6/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
  
Contents of sqm.out:

    
    
                --------------------------------------------------------
                                 AMBER SQM VERSION 19
     
                                         By
                  Ross C. Walker, Michael F. Crowley, Scott Brozell,
                             Tim Giese, Andreas W. Goetz,
                            Tai-Sung Lee and David A. Case
     
                --------------------------------------------------------
     
    
    --------------------------------------------------------------------------------
      QM CALCULATION INFO
    --------------------------------------------------------------------------------
    
    | QMMM: Citation for AMBER QMMM Run:
    | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
    
    QMMM: SINGLET STATE CALCULATION
    QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 83
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: F : M.J.S.DEWAR et al. THEOCHEM, 180, 1, (1988)
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    
    | QMMM: *** SCF convergence criteria ***
    | QMMM: Energy change                :  0.1D-09 kcal/mol
    | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    | QMMM: Density matrix change        :  0.5D-06
    | QMMM: Maximum number of SCF cycles :     1000
    
    | QMMM: *** Diagonalization Routine Information ***
    | QMMM: Pseudo diagonalizations are allowed.
    | QMMM: Auto diagonalization routine selection is in use.
    | QMMM:
    | QMMM: Timing diagonalization routines:
    | QMMM:                              norbs =      125
    | QMMM:    diag iterations used for timing =       10
    | QMMM:
    | QMMM:              Internal diag routine = 0.018883 seconds
    | QMMM:                 Dspev diag routine = 0.018975 seconds
    | QMMM:                Dspevd diag routine = 0.015131 seconds
    | QMMM:                Dspevx diag routine = 0.069844 seconds
    | QMMM:                 Dsyev diag routine = 0.020239 seconds
    | QMMM:                Dsyevd diag routine = 0.016122 seconds
    | QMMM:                Dsyevr diag routine = 0.017116 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.006072 seconds
    | QMMM:
    | QMMM: Using dspevd routine (diag_routine=3).
    
      QMMM: QM Region Cartesian Coordinates (*=link atom) 
      QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
      QMMM:     1        1      F      135.1190  107.8430  114.2820
      QMMM:     2        2      C      135.7000  108.9610  114.8430
      QMMM:     3        3      F      137.0630  108.8740  114.6380
      QMMM:     4        4      F      135.1540  110.0650  114.2240
      QMMM:     5        5      C      135.4660  108.9930  116.3440
      QMMM:     6        6      O      135.9880  107.9030  116.9990
      QMMM:     7        7      C      136.0230  107.6690  118.3640
      QMMM:     8        8      C      135.4750  108.6210  119.2960
      QMMM:     9        9      N      134.8960  109.7790  119.0770
      QMMM:    10       10      C      134.5490  110.3100  120.3070
      QMMM:    11       11      N      134.9150  109.4830  121.2580
      QMMM:    12       12      N      135.5000  108.4100  120.6520
      QMMM:    13       13      C      136.0760  107.2310  121.1150
      QMMM:    14       14      C      136.6080  106.3050  120.2550
      QMMM:    15       15      C      136.5920  106.5110  118.8280
      QMMM:    16       16      N      133.8980  111.5570  120.5090
      QMMM:    17       17      C      133.0430  112.2050  119.4990
      QMMM:    18       18      C      133.0670  113.7120  119.6060
      QMMM:    19       19      C      132.2400  114.4550  118.5650
      QMMM:    20       20      N      130.8720  113.9120  118.5270
      QMMM:    21       21      C      129.7720  114.8150  118.3380
      QMMM:    22       22      O      129.6090  115.6060  117.2740
      QMMM:    23       23      C      128.4830  116.2860  117.4740
      QMMM:    24       24      N      127.9570  115.9310  118.6230
      QMMM:    25       25      N      128.7760  114.9930  119.1770
      QMMM:    26       26      C      127.9090  117.3130  116.5130
      QMMM:    27       27      C      130.6340  112.4710  118.6910
      QMMM:    28       28      C      131.5750  111.9900  119.7850
      QMMM:    29       29      C      131.4650  112.7430  121.0950
      QMMM:    30       30      C      132.3660  113.9530  120.9260
      QMMM:    31       31      C      136.2380  110.2240  116.8460
      QMMM:    32       32      H      134.0270  112.0200  121.3860
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10    12826.8179 kcal/mol       51.1855 kcal/(mol*A)
    xmin    20    11664.3619 kcal/mol       36.4741 kcal/(mol*A)
    xmin    30    10764.5606 kcal/mol       40.6614 kcal/(mol*A)
    xmin    40     9962.7702 kcal/mol       25.8247 kcal/(mol*A)
    xmin    50     9275.0322 kcal/mol       18.6148 kcal/(mol*A)
    xmin    60     8822.9371 kcal/mol       14.9385 kcal/(mol*A)
    
    QMMM: ERROR!
    QMMM: Unable to achieve self consistency to the tolerances specified
    QMMM: No convergence in SCF after   1000 steps.
    QMMM: E =  -0.6485E+06 DeltaE =  -0.2844E+03 DeltaP =   0.1144E+01
    QMMM: Smallest DeltaE =  -0.1164E-09 DeltaP =   0.3721E-07 Step =      3
    
    

  
Failure running ANTECHAMBER for residue UNL Check reply log for details  

> ui tool show Axes/Planes/Centroids

> hide sel surfaces

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge -21) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpbf8j78dg/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpbf8j78dg/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpbf8j78dg/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Charges failed to converge using fast method; re-running using slower more
stable method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpbf8j78dg/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpbf8j78dg/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpbf8j78dg/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
  
Contents of sqm.out:

    
    
                --------------------------------------------------------
                                 AMBER SQM VERSION 19
     
                                         By
                  Ross C. Walker, Michael F. Crowley, Scott Brozell,
                             Tim Giese, Andreas W. Goetz,
                            Tai-Sung Lee and David A. Case
     
                --------------------------------------------------------
     
    
    --------------------------------------------------------------------------------
      QM CALCULATION INFO
    --------------------------------------------------------------------------------
    
    | QMMM: Citation for AMBER QMMM Run:
    | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
    
    QMMM: SINGLET STATE CALCULATION
    QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 83
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: F : M.J.S.DEWAR et al. THEOCHEM, 180, 1, (1988)
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    
    | QMMM: *** SCF convergence criteria ***
    | QMMM: Energy change                :  0.1D-09 kcal/mol
    | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    | QMMM: Density matrix change        :  0.5D-06
    | QMMM: Maximum number of SCF cycles :     1000
    
    | QMMM: *** Diagonalization Routine Information ***
    | QMMM: Pseudo diagonalizations are allowed.
    | QMMM: Auto diagonalization routine selection is in use.
    | QMMM:
    | QMMM: Timing diagonalization routines:
    | QMMM:                              norbs =      125
    | QMMM:    diag iterations used for timing =       10
    | QMMM:
    | QMMM:              Internal diag routine = 0.018757 seconds
    | QMMM:                 Dspev diag routine = 0.018926 seconds
    | QMMM:                Dspevd diag routine = 0.014980 seconds
    | QMMM:                Dspevx diag routine = 0.066449 seconds
    | QMMM:                 Dsyev diag routine = 0.019174 seconds
    | QMMM:                Dsyevd diag routine = 0.014969 seconds
    | QMMM:                Dsyevr diag routine = 0.016815 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.005908 seconds
    | QMMM:
    | QMMM: Using dsyevd routine (diag_routine=6).
    
      QMMM: QM Region Cartesian Coordinates (*=link atom) 
      QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
      QMMM:     1        1      F      135.1190  107.8430  114.2820
      QMMM:     2        2      C      135.7000  108.9610  114.8430
      QMMM:     3        3      F      137.0630  108.8740  114.6380
      QMMM:     4        4      F      135.1540  110.0650  114.2240
      QMMM:     5        5      C      135.4660  108.9930  116.3440
      QMMM:     6        6      O      135.9880  107.9030  116.9990
      QMMM:     7        7      C      136.0230  107.6690  118.3640
      QMMM:     8        8      C      135.4750  108.6210  119.2960
      QMMM:     9        9      N      134.8960  109.7790  119.0770
      QMMM:    10       10      C      134.5490  110.3100  120.3070
      QMMM:    11       11      N      134.9150  109.4830  121.2580
      QMMM:    12       12      N      135.5000  108.4100  120.6520
      QMMM:    13       13      C      136.0760  107.2310  121.1150
      QMMM:    14       14      C      136.6080  106.3050  120.2550
      QMMM:    15       15      C      136.5920  106.5110  118.8280
      QMMM:    16       16      N      133.8980  111.5570  120.5090
      QMMM:    17       17      C      133.0430  112.2050  119.4990
      QMMM:    18       18      C      133.0670  113.7120  119.6060
      QMMM:    19       19      C      132.2400  114.4550  118.5650
      QMMM:    20       20      N      130.8720  113.9120  118.5270
      QMMM:    21       21      C      129.7720  114.8150  118.3380
      QMMM:    22       22      O      129.6090  115.6060  117.2740
      QMMM:    23       23      C      128.4830  116.2860  117.4740
      QMMM:    24       24      N      127.9570  115.9310  118.6230
      QMMM:    25       25      N      128.7760  114.9930  119.1770
      QMMM:    26       26      C      127.9090  117.3130  116.5130
      QMMM:    27       27      C      130.6340  112.4710  118.6910
      QMMM:    28       28      C      131.5750  111.9900  119.7850
      QMMM:    29       29      C      131.4650  112.7430  121.0950
      QMMM:    30       30      C      132.3660  113.9530  120.9260
      QMMM:    31       31      C      136.2380  110.2240  116.8460
      QMMM:    32       32      H      134.0270  112.0200  121.3860
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10    12821.4744 kcal/mol       55.5689 kcal/(mol*A)
    xmin    20    11721.1896 kcal/mol       39.6261 kcal/(mol*A)
    xmin    30    10786.6874 kcal/mol       29.5214 kcal/(mol*A)
    xmin    40    10001.6909 kcal/mol       26.4068 kcal/(mol*A)
    xmin    50     9412.9744 kcal/mol       21.6764 kcal/(mol*A)
    xmin    60     8923.6069 kcal/mol       21.7947 kcal/(mol*A)
    xmin    70     8510.2694 kcal/mol       17.5595 kcal/(mol*A)
    
    QMMM: ERROR!
    QMMM: Unable to achieve self consistency to the tolerances specified
    QMMM: No convergence in SCF after   1000 steps.
    QMMM: E =  -0.6236E+06 DeltaE =  -0.2359E+03 DeltaP =   0.1128E+01
    QMMM: Smallest DeltaE =  -0.1164E-09 DeltaP =   0.3250E-05 Step =      5
    
    

  
Failure running ANTECHAMBER for residue UNL Check reply log for details  

> color bfactor sel

32 atoms, 1 residues, 1 surfaces, atom bfactor range 0 to 0  

> mlp sel

mlp: no amino acids specified  

> mlp sel

mlp: no amino acids specified  

> undo

> show sel surfaces

> color bfactor sel

32 atoms, 1 residues, 1 surfaces, atom bfactor range 0 to 0  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> ui tool show "Color Actions"

> color sel byhetero target s

> color sel byelement target s

> color sel byhetero target s

> color sel byelement target s

> color sel bychain target s

> color sel bynucleotide target s

> color sel bypolymer target s

> color sel cornflower blue target s

> color sel byhetero target s

> color sel purple target s

> color sel byelement target s

> color sel bynucleotide target s

> color sel bychain target s

> color sel byelement target s

> color sel byhetero target s

> hide sel surfaces

> color sel byhetero

> show sel surfaces

> rainbow sel

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge -21) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpf13ubf1f/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpf13ubf1f/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpf13ubf1f/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Charges failed to converge using fast method; re-running using slower more
stable method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpf13ubf1f/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpf13ubf1f/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpf13ubf1f/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
  
Contents of sqm.out:

    
    
                --------------------------------------------------------
                                 AMBER SQM VERSION 19
     
                                         By
                  Ross C. Walker, Michael F. Crowley, Scott Brozell,
                             Tim Giese, Andreas W. Goetz,
                            Tai-Sung Lee and David A. Case
     
                --------------------------------------------------------
     
    
    --------------------------------------------------------------------------------
      QM CALCULATION INFO
    --------------------------------------------------------------------------------
    
    | QMMM: Citation for AMBER QMMM Run:
    | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
    
    QMMM: SINGLET STATE CALCULATION
    QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 83
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: F : M.J.S.DEWAR et al. THEOCHEM, 180, 1, (1988)
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    
    | QMMM: *** SCF convergence criteria ***
    | QMMM: Energy change                :  0.1D-09 kcal/mol
    | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    | QMMM: Density matrix change        :  0.5D-06
    | QMMM: Maximum number of SCF cycles :     1000
    
    | QMMM: *** Diagonalization Routine Information ***
    | QMMM: Pseudo diagonalizations are allowed.
    | QMMM: Auto diagonalization routine selection is in use.
    | QMMM:
    | QMMM: Timing diagonalization routines:
    | QMMM:                              norbs =      125
    | QMMM:    diag iterations used for timing =       10
    | QMMM:
    | QMMM:              Internal diag routine = 0.019226 seconds
    | QMMM:                 Dspev diag routine = 0.017977 seconds
    | QMMM:                Dspevd diag routine = 0.013872 seconds
    | QMMM:                Dspevx diag routine = 0.067133 seconds
    | QMMM:                 Dsyev diag routine = 0.020374 seconds
    | QMMM:                Dsyevd diag routine = 0.016062 seconds
    | QMMM:                Dsyevr diag routine = 0.017449 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.006465 seconds
    | QMMM:
    | QMMM: Using dspevd routine (diag_routine=3).
    
      QMMM: QM Region Cartesian Coordinates (*=link atom) 
      QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
      QMMM:     1        1      F      135.1190  107.8430  114.2820
      QMMM:     2        2      C      135.7000  108.9610  114.8430
      QMMM:     3        3      F      137.0630  108.8740  114.6380
      QMMM:     4        4      F      135.1540  110.0650  114.2240
      QMMM:     5        5      C      135.4660  108.9930  116.3440
      QMMM:     6        6      O      135.9880  107.9030  116.9990
      QMMM:     7        7      C      136.0230  107.6690  118.3640
      QMMM:     8        8      C      135.4750  108.6210  119.2960
      QMMM:     9        9      N      134.8960  109.7790  119.0770
      QMMM:    10       10      C      134.5490  110.3100  120.3070
      QMMM:    11       11      N      134.9150  109.4830  121.2580
      QMMM:    12       12      N      135.5000  108.4100  120.6520
      QMMM:    13       13      C      136.0760  107.2310  121.1150
      QMMM:    14       14      C      136.6080  106.3050  120.2550
      QMMM:    15       15      C      136.5920  106.5110  118.8280
      QMMM:    16       16      N      133.8980  111.5570  120.5090
      QMMM:    17       17      C      133.0430  112.2050  119.4990
      QMMM:    18       18      C      133.0670  113.7120  119.6060
      QMMM:    19       19      C      132.2400  114.4550  118.5650
      QMMM:    20       20      N      130.8720  113.9120  118.5270
      QMMM:    21       21      C      129.7720  114.8150  118.3380
      QMMM:    22       22      O      129.6090  115.6060  117.2740
      QMMM:    23       23      C      128.4830  116.2860  117.4740
      QMMM:    24       24      N      127.9570  115.9310  118.6230
      QMMM:    25       25      N      128.7760  114.9930  119.1770
      QMMM:    26       26      C      127.9090  117.3130  116.5130
      QMMM:    27       27      C      130.6340  112.4710  118.6910
      QMMM:    28       28      C      131.5750  111.9900  119.7850
      QMMM:    29       29      C      131.4650  112.7430  121.0950
      QMMM:    30       30      C      132.3660  113.9530  120.9260
      QMMM:    31       31      C      136.2380  110.2240  116.8460
      QMMM:    32       32      H      134.0270  112.0200  121.3860
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10    12826.8179 kcal/mol       51.1855 kcal/(mol*A)
    xmin    20    11664.3619 kcal/mol       36.4741 kcal/(mol*A)
    xmin    30    10764.5606 kcal/mol       40.6614 kcal/(mol*A)
    xmin    40     9962.7702 kcal/mol       25.8247 kcal/(mol*A)
    xmin    50     9275.0322 kcal/mol       18.6148 kcal/(mol*A)
    xmin    60     8822.9371 kcal/mol       14.9385 kcal/(mol*A)
    
    QMMM: ERROR!
    QMMM: Unable to achieve self consistency to the tolerances specified
    QMMM: No convergence in SCF after   1000 steps.
    QMMM: E =  -0.6485E+06 DeltaE =  -0.2844E+03 DeltaP =   0.1144E+01
    QMMM: Smallest DeltaE =  -0.1164E-09 DeltaP =   0.3721E-07 Step =      3
    
    

  
Failure running ANTECHAMBER for residue UNL Check reply log for details  

> select clear

> hide #!10 surfaces

> show #!10 surfaces

> hide #!10 surfaces

> show #!10 surfaces

> hide #!10 surfaces

> show #!10 surfaces

> save /Users/u0154680/Documents/DailyWork/Roche_compound.png width 1344
> height 850 supersample 4 transparentBackground true

> show #!1 models

> hide #!10 models

> select ::name="GI9"

112 atoms, 120 bonds, 2 residues, 2 models selected  

> show #!1 atoms

> hide #!1 atoms

> select clear

> select ::name="GI9"

112 atoms, 120 bonds, 2 residues, 2 models selected  

> style #!1 stick

Changed 20874 atom styles  

> show #!1 atoms

> hide #!1 models

> show #!17 models

> hide #!17 models

> select
> ::name="AIB"::name="BMA"::name="BOC"::name="CLR"::name="FTO"::name="GI9"::name="GZR"::name="IGD"::name="JUU"::name="LIG"::name="LYN"::name="NAG"::name="PC1"::name="PTY"::name="UNL"::name="VLM"

7911 atoms, 8593 bonds, 330 residues, 128 models selected  

> show #!1 models

> show #!2 models

> hide #!1 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> show #!4 models

> style sel & #!4 stick

Changed 488 atom styles  

> style sel & #!4 stick

Changed 488 atom styles  

> select add #4

18432 atoms, 19399 bonds, 1 pseudobond, 1667 residues, 130 models selected  

> style sel & #!4 stick

Changed 11009 atom styles  

> show sel & #!4 cartoons

> hide #!4 models

> show #!15 models

> hide #!15 models

> show #!14 models

> hide #!14 models

> show #!17 models

> show #!16 models

> show #!15 models

> hide #!15 models

> hide #!17 models

> show sel & #!16 surfaces

> hide sel & #!16 surfaces

> hide sel & #!16 cartoons

> select clear

> show #!16 cartoons

> hide #!16 cartoons

> hide #!16 atoms

> show #!16 atoms

> select
> ::name="AIB"::name="BMA"::name="BOC"::name="CLR"::name="FTO"::name="GI9"::name="GZR"::name="IGD"::name="JUU"::name="LIG"::name="LYN"::name="NAG"::name="PC1"::name="PTY"::name="UNL"::name="VLM"

7911 atoms, 8593 bonds, 330 residues, 128 models selected  

> select ~sel

331193 atoms, 338118 bonds, 34 pseudobonds, 33782 residues, 41 models selected  

> hide sel & #!16 cartoons

> hide sel & #!16 atoms

> show sel & #!16 surfaces

> hide sel & #!16 surfaces

> select clear

> select ::name="LIG"

170 atoms, 190 bonds, 5 residues, 5 models selected  

> show #!16 atoms

> hide #!16 atoms

> show #!16 atoms

> select
> ::name="AIB"::name="BMA"::name="BOC"::name="CLR"::name="FTO"::name="GI9"::name="GZR"::name="IGD"::name="JUU"::name="LIG"::name="LYN"::name="NAG"::name="PC1"::name="PTY"::name="UNL"::name="VLM"

7911 atoms, 8593 bonds, 330 residues, 128 models selected  

> select ~sel

331193 atoms, 338118 bonds, 34 pseudobonds, 33782 residues, 42 models selected  

> hide sel & #!16 atoms

> show sel & #!16 surfaces

> hide sel & #!16 surfaces

> select clear

> select
> ::name="AIB"::name="BMA"::name="BOC"::name="CLR"::name="FTO"::name="GI9"::name="GZR"::name="IGD"::name="JUU"::name="LIG"::name="LYN"::name="NAG"::name="PC1"::name="PTY"::name="UNL"::name="VLM"

7911 atoms, 8593 bonds, 330 residues, 128 models selected  

> show sel & #!16 surfaces

> select clear

> select ::name="AIB"

18 atoms, 15 bonds, 3 residues, 1 model selected  

> select ::name="BMA"

264 atoms, 280 bonds, 24 residues, 8 models selected  

> select ::name="BOC"

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select ::name="IGD"

32 atoms, 34 bonds, 1 residue, 1 model selected  

> select ::name="FTO"

49 atoms, 51 bonds, 1 residue, 1 model selected  

> select ::name="CLR"

616 atoms, 682 bonds, 22 residues, 8 models selected  

> select ::name="JUU"

22 atoms, 23 bonds, 1 residue, 1 model selected  

> select ::name="GZR"

31 atoms, 34 bonds, 1 residue, 1 model selected  

> select ::name="LYN"

44 atoms, 42 bonds, 2 residues, 1 model selected  

> select ::name="NAG"

1877 atoms, 1920 bonds, 134 residues, 8 models selected  

> hide sel & #!16 surfaces

> hide sel & #!16 atoms

> select ::name="PC1"

773 atoms, 754 bonds, 19 residues, 8 models selected  

> hide sel & #!16 surfaces

> hide sel & #!16 cartoons

> hide sel & #!16 atoms

> select ::name="VLM"

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select ::name="UNL"

3844 atoms, 4385 bonds, 112 residues, 112 models selected  

> select ::name="FTO"

49 atoms, 51 bonds, 1 residue, 1 model selected  

> select ::name="CLR"

616 atoms, 682 bonds, 22 residues, 8 models selected  

> select ::name="PTY"

44 atoms, 43 bonds, 1 residue, 1 model selected  

> hide sel surfaces

> hide sel atoms

> select ::name="GZR"

31 atoms, 34 bonds, 1 residue, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue GZR (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpyoipe1dd/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpyoipe1dd/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(GZR) ``  
(GZR) `Welcome to antechamber 20.0: molecular input file processor.`  
(GZR) ``  
(GZR) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpyoipe1dd/ante.in.mol2);
atoms read (63), bonds read (66).`  
(GZR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(GZR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(GZR) ``  
(GZR) ``  
(GZR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(GZR) `Info: Total number of electrons: 228; net charge: 0`  
(GZR) ``  
(GZR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(GZR) ``  
(GZR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(GZR) ``  
(GZR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(GZR) ``  
Charges for residue GZR determined  
Coulombic values for 7d8x_B SES surface #16.3: minimum, -3.32, mean -0.18,
maximum 1.31  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select ::name="AIB"

18 atoms, 15 bonds, 3 residues, 1 model selected  

> select ::name="BMA"

264 atoms, 280 bonds, 24 residues, 8 models selected  

> select ::name="CLR"

616 atoms, 682 bonds, 22 residues, 8 models selected  

> hide sel & #!16 surfaces

> hide sel & #!16 atoms

> select ::name="JUU"

22 atoms, 23 bonds, 1 residue, 1 model selected  

> select ::name="LYN"

44 atoms, 42 bonds, 2 residues, 1 model selected  

> select ::name="PTY"

44 atoms, 43 bonds, 1 residue, 1 model selected  

> select ::name="VLM"

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select ::name="IGD"

32 atoms, 34 bonds, 1 residue, 1 model selected  

> select ::name="CLR"

616 atoms, 682 bonds, 22 residues, 8 models selected  

> select ::name="BOC"

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select ::name="BMA"

264 atoms, 280 bonds, 24 residues, 8 models selected  

> select ::name="NAG"

1877 atoms, 1920 bonds, 134 residues, 8 models selected  

> select ::name="PC1"

773 atoms, 754 bonds, 19 residues, 8 models selected  

> select ::name="PTY"

44 atoms, 43 bonds, 1 residue, 1 model selected  

> select ::name="UNL"

3844 atoms, 4385 bonds, 112 residues, 112 models selected  

> select ::name="BMA"

264 atoms, 280 bonds, 24 residues, 8 models selected  

> select ::name="FTO"

49 atoms, 51 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select ::name="FTO"

49 atoms, 51 bonds, 1 residue, 1 model selected  

> select ::name="IGD"

32 atoms, 34 bonds, 1 residue, 1 model selected  

> select ::name="NAG"

1877 atoms, 1920 bonds, 134 residues, 8 models selected  

> select ::name="NAG"

1877 atoms, 1920 bonds, 134 residues, 8 models selected  

> select ::name="PC1"

773 atoms, 754 bonds, 19 residues, 8 models selected  

> select ::name="UNL"

3844 atoms, 4385 bonds, 112 residues, 112 models selected  

> select ::name="VLM"

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select ::name="GZR"

31 atoms, 34 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> hide #!16 surfaces

> show #!16 surfaces

> hide #!16 surfaces

> select ::name="GZR"

31 atoms, 34 bonds, 1 residue, 1 model selected  

> show sel surfaces

> select clear

> save /Users/u0154680/Documents/DailyWork/Arylimidazole_compound.png width
> 1344 height 850 supersample 4 transparentBackground true

> show #12 models

> hide #12 models

> show #!11 models

> hide #!11 models

> show #12 models

> hide #12 models

> show #!10 models

> hide #!10 models

> show #!10 models

> save /Users/u0154680/Documents/DailyWork/overlap.png width 1344 height 850
> supersample 4 transparentBackground true

> hide #!10,16 surfaces

> hide #!10 models

> show #!10 models

> hide #!10 models

> hide #!16 models

> show #!16 models

> show #12 models

> hide #12 models

> show #!11 models

> show #!17 models

> hide #!17 models

> show #!15 models

> hide #!15 models

> show #!13 models

> hide #!13 models

> show #12 models

> hide #12 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!21 models

> select ::name="GI9"

112 atoms, 120 bonds, 2 residues, 2 models selected  

> show sel & #!21 surfaces

> coulombic sel & #!21

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue GI9 (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmp4hbc0b88/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmp4hbc0b88/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(GI9) ``  
(GI9) `Welcome to antechamber 20.0: molecular input file processor.`  
(GI9) ``  
(GI9) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmp4hbc0b88/ante.in.mol2);
atoms read (56), bonds read (60).`  
(GI9) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(GI9) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(GI9) ``  
(GI9) ``  
(GI9) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(GI9) `Info: Total number of electrons: 244; net charge: 0`  
(GI9) ``  
(GI9) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(GI9) ``  
(GI9) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(GI9) ``  
(GI9) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(GI9) ``  
Charges for residue GI9 determined  
Coulombic values for RSR57_Modified_ResiduesSC_Abeta46_GSM3.pdb_B SES surface
#21.2: minimum, -3.32, mean 0.06, maximum 3.29  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select clear

> hide #!16 models

> show #20 models

> hide #20 models

> hide #!21 models

> show #!21 models

> hide #!11 models

> set bgColor white

> lighting simple

> lighting soft

> lighting full

> lighting simple

> lighting flat

> graphics silhouettes false

> lighting full

> lighting soft

> lighting full

> lighting simple

> select ::name="GI9"

112 atoms, 120 bonds, 2 residues, 2 models selected  

> view sel

> select clear

> hide #!21 models

> show #!16 models

> hide #!16 models

> show #12 models

> hide #12 models

> show #!11 models

> select add #11

32 atoms, 36 bonds, 1 residue, 1 model selected  

> show sel surfaces

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge -21) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpk7go74_m/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpk7go74_m/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpk7go74_m/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Charges failed to converge using fast method; re-running using slower more
stable method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpk7go74_m/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpk7go74_m/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpk7go74_m/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
  
Contents of sqm.out:

    
    
                --------------------------------------------------------
                                 AMBER SQM VERSION 19
     
                                         By
                  Ross C. Walker, Michael F. Crowley, Scott Brozell,
                             Tim Giese, Andreas W. Goetz,
                            Tai-Sung Lee and David A. Case
     
                --------------------------------------------------------
     
    
    --------------------------------------------------------------------------------
      QM CALCULATION INFO
    --------------------------------------------------------------------------------
    
    | QMMM: Citation for AMBER QMMM Run:
    | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
    
    QMMM: SINGLET STATE CALCULATION
    QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 83
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: F : M.J.S.DEWAR et al. THEOCHEM, 180, 1, (1988)
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    
    | QMMM: *** SCF convergence criteria ***
    | QMMM: Energy change                :  0.1D-09 kcal/mol
    | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    | QMMM: Density matrix change        :  0.5D-06
    | QMMM: Maximum number of SCF cycles :     1000
    
    | QMMM: *** Diagonalization Routine Information ***
    | QMMM: Pseudo diagonalizations are allowed.
    | QMMM: Auto diagonalization routine selection is in use.
    | QMMM:
    | QMMM: Timing diagonalization routines:
    | QMMM:                              norbs =      125
    | QMMM:    diag iterations used for timing =       10
    | QMMM:
    | QMMM:              Internal diag routine = 0.020377 seconds
    | QMMM:                 Dspev diag routine = 0.020156 seconds
    | QMMM:                Dspevd diag routine = 0.015102 seconds
    | QMMM:                Dspevx diag routine = 0.068023 seconds
    | QMMM:                 Dsyev diag routine = 0.020468 seconds
    | QMMM:                Dsyevd diag routine = 0.016342 seconds
    | QMMM:                Dsyevr diag routine = 0.016872 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.005994 seconds
    | QMMM:
    | QMMM: Using dspevd routine (diag_routine=3).
    
      QMMM: QM Region Cartesian Coordinates (*=link atom) 
      QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
      QMMM:     1        1      F      136.9680  109.5600  114.8930
      QMMM:     2        2      C      136.7510  108.2080  114.7240
      QMMM:     3        3      F      135.4520  108.0440  114.2850
      QMMM:     4        4      F      137.6680  107.7550  113.8010
      QMMM:     5        5      C      136.8810  107.4730  116.0460
      QMMM:     6        6      O      135.9880  107.9030  116.9990
      QMMM:     7        7      C      136.0230  107.6690  118.3640
      QMMM:     8        8      C      135.4750  108.6210  119.2960
      QMMM:     9        9      N      134.8960  109.7790  119.0770
      QMMM:    10       10      C      134.5490  110.3100  120.3070
      QMMM:    11       11      N      134.9150  109.4830  121.2580
      QMMM:    12       12      N      135.5000  108.4100  120.6520
      QMMM:    13       13      C      136.0760  107.2310  121.1150
      QMMM:    14       14      C      136.6080  106.3050  120.2550
      QMMM:    15       15      C      136.5920  106.5110  118.8280
      QMMM:    16       16      N      133.8980  111.5570  120.5090
      QMMM:    17       17      C      133.0430  112.2050  119.4990
      QMMM:    18       18      C      133.0670  113.7120  119.6060
      QMMM:    19       19      C      132.2400  114.4550  118.5650
      QMMM:    20       20      N      130.8720  113.9120  118.5270
      QMMM:    21       21      C      129.7720  114.8150  118.3380
      QMMM:    22       22      O      129.6090  115.6060  117.2740
      QMMM:    23       23      C      128.4830  116.2860  117.4740
      QMMM:    24       24      N      127.9570  115.9310  118.6230
      QMMM:    25       25      N      128.7760  114.9930  119.1770
      QMMM:    26       26      C      127.9090  117.3130  116.5130
      QMMM:    27       27      C      130.6340  112.4710  118.6910
      QMMM:    28       28      C      131.5750  111.9900  119.7850
      QMMM:    29       29      C      131.4650  112.7430  121.0950
      QMMM:    30       30      C      132.3660  113.9530  120.9260
      QMMM:    31       31      C      136.5250  106.0110  115.7320
      QMMM:    32       32      H      134.0270  112.0200  121.3860
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10    12230.9625 kcal/mol       62.1005 kcal/(mol*A)
    
    QMMM: ERROR!
    QMMM: Unable to achieve self consistency to the tolerances specified
    QMMM: No convergence in SCF after   1000 steps.
    QMMM: E =  -0.7491E+06 DeltaE =   0.7633E+02 DeltaP =   0.9661E+00
    QMMM: Smallest DeltaE =  -0.5553E-07 DeltaP =   0.2620E-05 Step =      2
    
    

  
Failure running ANTECHAMBER for residue UNL Check reply log for details  

> hide #!11 models

> show #12 models

> hide #12 models

> show #!11 models

> show #!10 models

> select subtract #11

1 model selected  

> hide #!11 models

> select add #10

32 atoms, 36 bonds, 1 residue, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge -21) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpjk43sp31/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpjk43sp31/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpjk43sp31/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Charges failed to converge using fast method; re-running using slower more
stable method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpjk43sp31/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpjk43sp31/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpjk43sp31/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
  
Contents of sqm.out:

    
    
                --------------------------------------------------------
                                 AMBER SQM VERSION 19
     
                                         By
                  Ross C. Walker, Michael F. Crowley, Scott Brozell,
                             Tim Giese, Andreas W. Goetz,
                            Tai-Sung Lee and David A. Case
     
                --------------------------------------------------------
     
    
    --------------------------------------------------------------------------------
      QM CALCULATION INFO
    --------------------------------------------------------------------------------
    
    | QMMM: Citation for AMBER QMMM Run:
    | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
    
    QMMM: SINGLET STATE CALCULATION
    QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 83
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: F : M.J.S.DEWAR et al. THEOCHEM, 180, 1, (1988)
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    
    | QMMM: *** SCF convergence criteria ***
    | QMMM: Energy change                :  0.1D-09 kcal/mol
    | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    | QMMM: Density matrix change        :  0.5D-06
    | QMMM: Maximum number of SCF cycles :     1000
    
    | QMMM: *** Diagonalization Routine Information ***
    | QMMM: Pseudo diagonalizations are allowed.
    | QMMM: Auto diagonalization routine selection is in use.
    | QMMM:
    | QMMM: Timing diagonalization routines:
    | QMMM:                              norbs =      125
    | QMMM:    diag iterations used for timing =       10
    | QMMM:
    | QMMM:              Internal diag routine = 0.019394 seconds
    | QMMM:                 Dspev diag routine = 0.020113 seconds
    | QMMM:                Dspevd diag routine = 0.015446 seconds
    | QMMM:                Dspevx diag routine = 0.066258 seconds
    | QMMM:                 Dsyev diag routine = 0.020318 seconds
    | QMMM:                Dsyevd diag routine = 0.016198 seconds
    | QMMM:                Dsyevr diag routine = 0.017531 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.006345 seconds
    | QMMM:
    | QMMM: Using dspevd routine (diag_routine=3).
    
      QMMM: QM Region Cartesian Coordinates (*=link atom) 
      QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
      QMMM:     1        1      F      135.1190  107.8430  114.2820
      QMMM:     2        2      C      135.7000  108.9610  114.8430
      QMMM:     3        3      F      137.0630  108.8740  114.6380
      QMMM:     4        4      F      135.1540  110.0650  114.2240
      QMMM:     5        5      C      135.4660  108.9930  116.3440
      QMMM:     6        6      O      135.9880  107.9030  116.9990
      QMMM:     7        7      C      136.0230  107.6690  118.3640
      QMMM:     8        8      C      135.4750  108.6210  119.2960
      QMMM:     9        9      N      134.8960  109.7790  119.0770
      QMMM:    10       10      C      134.5490  110.3100  120.3070
      QMMM:    11       11      N      134.9150  109.4830  121.2580
      QMMM:    12       12      N      135.5000  108.4100  120.6520
      QMMM:    13       13      C      136.0760  107.2310  121.1150
      QMMM:    14       14      C      136.6080  106.3050  120.2550
      QMMM:    15       15      C      136.5920  106.5110  118.8280
      QMMM:    16       16      N      133.8980  111.5570  120.5090
      QMMM:    17       17      C      133.0430  112.2050  119.4990
      QMMM:    18       18      C      133.0670  113.7120  119.6060
      QMMM:    19       19      C      132.2400  114.4550  118.5650
      QMMM:    20       20      N      130.8720  113.9120  118.5270
      QMMM:    21       21      C      129.7720  114.8150  118.3380
      QMMM:    22       22      O      129.6090  115.6060  117.2740
      QMMM:    23       23      C      128.4830  116.2860  117.4740
      QMMM:    24       24      N      127.9570  115.9310  118.6230
      QMMM:    25       25      N      128.7760  114.9930  119.1770
      QMMM:    26       26      C      127.9090  117.3130  116.5130
      QMMM:    27       27      C      130.6340  112.4710  118.6910
      QMMM:    28       28      C      131.5750  111.9900  119.7850
      QMMM:    29       29      C      131.4650  112.7430  121.0950
      QMMM:    30       30      C      132.3660  113.9530  120.9260
      QMMM:    31       31      C      136.2380  110.2240  116.8460
      QMMM:    32       32      H      134.0270  112.0200  121.3860
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10    12826.8179 kcal/mol       51.1855 kcal/(mol*A)
    xmin    20    11664.3619 kcal/mol       36.4741 kcal/(mol*A)
    xmin    30    10764.5606 kcal/mol       40.6614 kcal/(mol*A)
    xmin    40     9962.7702 kcal/mol       25.8247 kcal/(mol*A)
    xmin    50     9275.0322 kcal/mol       18.6148 kcal/(mol*A)
    xmin    60     8822.9371 kcal/mol       14.9385 kcal/(mol*A)
    
    QMMM: ERROR!
    QMMM: Unable to achieve self consistency to the tolerances specified
    QMMM: No convergence in SCF after   1000 steps.
    QMMM: E =  -0.6485E+06 DeltaE =  -0.2844E+03 DeltaP =   0.1144E+01
    QMMM: Smallest DeltaE =  -0.1164E-09 DeltaP =   0.3721E-07 Step =      3
    
    

  
Failure running ANTECHAMBER for residue UNL Check reply log for details  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
> sqm.out

Unknown command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out  

> "/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
> sqm.out"

Unknown command: "/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out"  

> sqm -O -i sqm.in -o sqm.out"

Unknown command: sqm -O -i sqm.in -o sqm.out"  

> sqm -O -i sqm.in -o sqm.out"

Unknown command: sqm -O -i sqm.in -o sqm.out"  

> hide #!10 models

> select subtract #10

1 model selected  

> show #!1 models

> hide #!1 models

> show #!18 models

> hide #!18 models

> show #!17 models

> hide #!17 models

> show #!16 models

> show #!15 models

> hide #!15 models

> show #!14 models

> hide #!14 models

> show #!13 models

> hide #!13 models

> show #9 models

> hide #9 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #6.1 models

> hide #6.1 models

> hide #!6 models

> show #6.1 models

> hide #6.1 models

> show #6.2 models

> hide #!6 models

> show #6.5 models

> hide #6.5 models

> hide #!6 models

> select add #6.2

34 atoms, 39 bonds, 1 residue, 1 model selected  

> hide #6.2 models

> show #6.2 models

> hide #!6 models

> show #!6 models

> select add #6

3780 atoms, 4313 bonds, 110 residues, 111 models selected  

> select subtract #6.2

3746 atoms, 4274 bonds, 109 residues, 110 models selected  

> hide #6.2 models

> select add #6

3780 atoms, 4313 bonds, 110 residues, 111 models selected  

> select subtract #6

Nothing selected  

> select add #6

3780 atoms, 4313 bonds, 110 residues, 111 models selected  

> select subtract #6

Nothing selected  

> hide #!6 models

> show #!6 models

> select add #6

3780 atoms, 4313 bonds, 110 residues, 111 models selected  

> select subtract #6

Nothing selected  

> hide #!6 models

> show #6.6 models

> select add #6.6

28 atoms, 32 bonds, 1 residue, 1 model selected  

> show sel surfaces

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge +0) with am1-bcc method  
UNL: number of electrons (209) + formal charge (+0) is odd; cannot compute
charges for radical species using AM1-BCC method  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpx80jvg3o/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpx80jvg3o/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpx80jvg3o/ante.in.mol2);
atoms read (52), bonds read (56).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 210; net charge: 0`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(UNL) ``  
Charges for residue UNL determined  
Coulombic values for C21H24ClN5O_ SES surface #6.6.1: minimum, -3.74, mean
0.07, maximum 2.09  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!6 models

> show #!6 models

> hide #6.28 models

> show #6.28 models

> hide #6.28 models

> hide #!16 models

> view sel

> select clear

> lighting simple

> lighting soft

> lighting flat

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

> graphics silhouettes false

> lighting simple

> graphics silhouettes true

> show #12 models

> hide #12 models

> show #!11 models

> show #12 models

> hide #12 models

> show #!10 models

> hide #!6 models

> hide #!10 models

> hide #!11 models

> show #!10 models

> show #!10 surfaces

> coulombic #!10

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge -21) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpjp4tw2xm/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpjp4tw2xm/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpjp4tw2xm/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Charges failed to converge using fast method; re-running using slower more
stable method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpjp4tw2xm/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpjp4tw2xm/ante.out.mol2 -fo
mol2 -c bcc -nc -21 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmpjp4tw2xm/ante.in.mol2);
atoms read (32), bonds read (36).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 228; net charge: -21`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) `/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
  
Contents of sqm.out:

    
    
                --------------------------------------------------------
                                 AMBER SQM VERSION 19
     
                                         By
                  Ross C. Walker, Michael F. Crowley, Scott Brozell,
                             Tim Giese, Andreas W. Goetz,
                            Tai-Sung Lee and David A. Case
     
                --------------------------------------------------------
     
    
    --------------------------------------------------------------------------------
      QM CALCULATION INFO
    --------------------------------------------------------------------------------
    
    | QMMM: Citation for AMBER QMMM Run:
    | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
    
    QMMM: SINGLET STATE CALCULATION
    QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 83
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: F : M.J.S.DEWAR et al. THEOCHEM, 180, 1, (1988)
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    
    | QMMM: *** SCF convergence criteria ***
    | QMMM: Energy change                :  0.1D-09 kcal/mol
    | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    | QMMM: Density matrix change        :  0.5D-06
    | QMMM: Maximum number of SCF cycles :     1000
    
    | QMMM: *** Diagonalization Routine Information ***
    | QMMM: Pseudo diagonalizations are allowed.
    | QMMM: Auto diagonalization routine selection is in use.
    | QMMM:
    | QMMM: Timing diagonalization routines:
    | QMMM:                              norbs =      125
    | QMMM:    diag iterations used for timing =       10
    | QMMM:
    | QMMM:              Internal diag routine = 0.019954 seconds
    | QMMM:                 Dspev diag routine = 0.020169 seconds
    | QMMM:                Dspevd diag routine = 0.015034 seconds
    | QMMM:                Dspevx diag routine = 0.066529 seconds
    | QMMM:                 Dsyev diag routine = 0.020264 seconds
    | QMMM:                Dsyevd diag routine = 0.015979 seconds
    | QMMM:                Dsyevr diag routine = 0.018026 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.006359 seconds
    | QMMM:
    | QMMM: Using dspevd routine (diag_routine=3).
    
      QMMM: QM Region Cartesian Coordinates (*=link atom) 
      QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
      QMMM:     1        1      F      135.1190  107.8430  114.2820
      QMMM:     2        2      C      135.7000  108.9610  114.8430
      QMMM:     3        3      F      137.0630  108.8740  114.6380
      QMMM:     4        4      F      135.1540  110.0650  114.2240
      QMMM:     5        5      C      135.4660  108.9930  116.3440
      QMMM:     6        6      O      135.9880  107.9030  116.9990
      QMMM:     7        7      C      136.0230  107.6690  118.3640
      QMMM:     8        8      C      135.4750  108.6210  119.2960
      QMMM:     9        9      N      134.8960  109.7790  119.0770
      QMMM:    10       10      C      134.5490  110.3100  120.3070
      QMMM:    11       11      N      134.9150  109.4830  121.2580
      QMMM:    12       12      N      135.5000  108.4100  120.6520
      QMMM:    13       13      C      136.0760  107.2310  121.1150
      QMMM:    14       14      C      136.6080  106.3050  120.2550
      QMMM:    15       15      C      136.5920  106.5110  118.8280
      QMMM:    16       16      N      133.8980  111.5570  120.5090
      QMMM:    17       17      C      133.0430  112.2050  119.4990
      QMMM:    18       18      C      133.0670  113.7120  119.6060
      QMMM:    19       19      C      132.2400  114.4550  118.5650
      QMMM:    20       20      N      130.8720  113.9120  118.5270
      QMMM:    21       21      C      129.7720  114.8150  118.3380
      QMMM:    22       22      O      129.6090  115.6060  117.2740
      QMMM:    23       23      C      128.4830  116.2860  117.4740
      QMMM:    24       24      N      127.9570  115.9310  118.6230
      QMMM:    25       25      N      128.7760  114.9930  119.1770
      QMMM:    26       26      C      127.9090  117.3130  116.5130
      QMMM:    27       27      C      130.6340  112.4710  118.6910
      QMMM:    28       28      C      131.5750  111.9900  119.7850
      QMMM:    29       29      C      131.4650  112.7430  121.0950
      QMMM:    30       30      C      132.3660  113.9530  120.9260
      QMMM:    31       31      C      136.2380  110.2240  116.8460
      QMMM:    32       32      H      134.0270  112.0200  121.3860
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10    12826.8179 kcal/mol       51.1855 kcal/(mol*A)
    xmin    20    11664.3619 kcal/mol       36.4741 kcal/(mol*A)
    xmin    30    10764.5606 kcal/mol       40.6614 kcal/(mol*A)
    xmin    40     9962.7702 kcal/mol       25.8247 kcal/(mol*A)
    xmin    50     9275.0322 kcal/mol       18.6148 kcal/(mol*A)
    xmin    60     8822.9371 kcal/mol       14.9385 kcal/(mol*A)
    
    QMMM: ERROR!
    QMMM: Unable to achieve self consistency to the tolerances specified
    QMMM: No convergence in SCF after   1000 steps.
    QMMM: E =  -0.6485E+06 DeltaE =  -0.2844E+03 DeltaP =   0.1144E+01
    QMMM: Smallest DeltaE =  -0.1164E-09 DeltaP =   0.3721E-07 Step =      3
    
    

  
Failure running ANTECHAMBER for residue UNL Check reply log for details  

> show #!6 models

> hide #!6.6 models

> show #6.5 models

> hide #!10 models

> show #!10 models

> hide #6.5#!10 surfaces

> show #6.1 models

> hide #6.1 models

> show #6.4 models

> hide #6.5 models

> hide #6.4 models

> show #6.3 models

> hide #6.3 models

> show #6.2 models

> hide #6.2 models

> show #!6.6 models

> hide #!6.6 models

> show #6.8 models

> hide #6.8 models

> show #6.10 models

> hide #6.10 models

> show #6.12 models

> hide #6.12 models

> show #6.12 models

> hide #6.12 models

> show #6.13 models

> hide #6.13 models

> select add #6.15

34 atoms, 39 bonds, 1 residue, 1 model selected  

> select subtract #6.15

Nothing selected  

> show #6.15 models

> hide #6.15 models

> show #6.16 models

> hide #6.16 models

> show #6.16 models

> hide #6.16 models

> show #6.22 models

> hide #6.22 models

> show #6.24 models

> hide #6.24 models

> show #6.28 models

> hide #6.28 models

> show #6.29 models

> hide #6.29 models

> show #6.30 models

> hide #6.30 models

> show #6.30 models

> hide #6.30 models

> show #6.30 models

> hide #6.30 models

> show #6.26 models

> show #6.30 models

> hide #6.30 models

> hide #6.26 models

> show #6.32 models

> hide #6.32 models

> show #6.36 models

> hide #6.36 models

> show #6.38 models

> hide #6.38 models

> show #6.37 models

> hide #6.37 models

> show #6.37 models

> hide #6.37 models

> show #6.40 models

> hide #6.40 models

> show #6.39 models

> hide #6.39 models

> show #6.42 models

> hide #6.42 models

> show #6.43 models

> hide #6.43 models

> show #6.47 models

> hide #6.47 models

> show #6.49 models

> hide #6.49 models

> show #6.48 models

> hide #6.48 models

> show #6.50 models

> hide #6.50 models

> show #6.51 models

> hide #6.51 models

> show #6.53 models

> hide #6.53 models

> show #6.55 models

> hide #6.55 models

> show #6.57 models

> hide #6.57 models

> show #6.58 models

> hide #6.58 models

> show #6.59 models

> hide #!10 models

> show #!10 models

> save /Users/u0154680/Documents/DailyWork/overlap2.png width 1344 height 827
> supersample 4 transparentBackground true

> hide #!10 models

> select add #6.59

33 atoms, 38 bonds, 1 residue, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmp48a9vr3y/ante.in.mol2 -fi
mol2 -o
/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmp48a9vr3y/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/d3/m_3b1byn6sqgp32k2fz8m135mfj8dc/T/tmp48a9vr3y/ante.in.mol2);
atoms read (57), bonds read (62).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 238; net charge: 0`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(UNL) ``  
Charges for residue UNL determined  
Coulombic values for FPB_31_1_ SES surface #6.59.1: minimum, -2.59, mean
-0.26, maximum 1.75  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select clear

> select add #6.59

33 atoms, 38 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> graphics silhouettes false

> view

> lighting simple

> ui tool show "Side View"

> view

> ui tool show "Side View"

> set bgColor gray

> hide #!6 models

> show #!11 models

> hide #!11 models

> show #!10 models

> show #!21 models

> show #!18 models

> hide #!18 models

> show #12 models

> hide #12 models

> show #!11 models

> hide #!11 models

> show #9 models

> hide #9 models

> hide #!10 models

> select subtract #19

Nothing selected  

> hide #!21 models

> show #!21 models

> show #!18 models

> hide #!21 models

> show #!21 models

> show #!1 models

> show #!1,18,21 cartoons

> hide #!1 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> hide #!21 models

> show #!21 models

> show #!21 atoms

> show #!1 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!21 models

> hide #!1 models

> show #!18 atoms

> show #!1 models

> select ::name="GI9"

112 atoms, 120 bonds, 2 residues, 2 models selected  

Window position QRect(995,-640 339x144) outside any known screen, using
primary screen  

> select sel : select ~sel

327242 atoms, 333955 bonds, 29 pseudobonds, 33256 residues, 40 models selected  

> hide sel & #!1,18 atoms

> hide sel & #!1,18 cartoons

> hide #!1 models

> show #!1 models

> open
> /Volumes/gbw_lvs/GBW-0009_VIB_DS_Images/Carlos_L/Projects/GSEC/In_Silico/Structure/RSR57_Modified_ResiduesSC_Abeta46_GSM3.pdb

Chain information for RSR57_Modified_ResiduesSC_Abeta46_GSM3.pdb #32  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style sel & #!1,18 stick

Changed 41094 atom styles  

> style sel & #!1,18 stick

Changed 41094 atom styles  

> select clear

> style #!1,18,32 stick

Changed 63114 atom styles  

> hide #!18 models

> hide #!1 models

> show #!1 models

> close #32

> show #!18 models

> ui tool show Rotamers

> select #18/B:240@OH

1 atom, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel TYR rotLib Dunbrack

RSR57_Modified_with_Abeta46_GSM3.pdb #18/B TYR 240: phi -78.2, psi -19.6 trans  
Changed 180 bond radii  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

385 atoms, 387 bonds, 22 residues, 1 model selected  

> select up

3627 atoms, 3671 bonds, 219 residues, 1 model selected  

> select up

3698 atoms, 3741 bonds, 224 residues, 1 model selected  

> select up

5045 atoms, 5108 bonds, 309 residues, 1 model selected  

> select up

5101 atoms, 5168 bonds, 310 residues, 1 model selected  

> select up

21120 atoms, 21398 bonds, 1333 residues, 1 model selected  

> select up

334984 atoms, 342156 bonds, 16 pseudobonds, 33956 residues, 30 models selected  

> select up

334984 atoms, 342156 bonds, 16 pseudobonds, 33956 residues, 51 models selected  

> select up

334984 atoms, 342156 bonds, 17 pseudobonds, 33956 residues, 52 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select up

334984 atoms, 342156 bonds, 20 pseudobonds, 33956 residues, 53 models selected  

> select down

334984 atoms, 342156 bonds, 17 pseudobonds, 33956 residues, 52 models selected  

> select down

334984 atoms, 342156 bonds, 16 pseudobonds, 33956 residues, 51 models selected  

> select down

334984 atoms, 342156 bonds, 16 pseudobonds, 33956 residues, 51 models selected  

> select up

334984 atoms, 342156 bonds, 16 pseudobonds, 33956 residues, 51 models selected  

> select down

334984 atoms, 342156 bonds, 16 pseudobonds, 33956 residues, 51 models selected  

> select down

21120 atoms, 21398 bonds, 1333 residues, 22 models selected  

> select down

5101 atoms, 5168 bonds, 310 residues, 22 models selected  

> select down

5045 atoms, 5108 bonds, 309 residues, 1 model selected  

> select down

3698 atoms, 3741 bonds, 224 residues, 1 model selected  

> select down

3627 atoms, 3671 bonds, 219 residues, 1 model selected  

> select down

385 atoms, 387 bonds, 22 residues, 1 model selected  

> select down

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

385 atoms, 387 bonds, 22 residues, 1 model selected  

> select up

3627 atoms, 3671 bonds, 219 residues, 1 model selected  

> select down

385 atoms, 387 bonds, 22 residues, 1 model selected  

> select down

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> hide #!1 models

> show #!1 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> select #1/B:240@HE2

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

385 atoms, 387 bonds, 22 residues, 1 model selected  

> select clear

> select #1/B:240@HH

1 atom, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel TYR rotLib Dunbrack

RSR57.pdb #1/B TYR 240: phi -78.2, psi -19.6 trans  
Changed 180 bond radii  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

385 atoms, 387 bonds, 22 residues, 1 model selected  

> select up

3626 atoms, 3670 bonds, 219 residues, 1 model selected  

> select up

3697 atoms, 3740 bonds, 224 residues, 1 model selected  

> select up

5043 atoms, 5106 bonds, 309 residues, 1 model selected  

> swapaa #!1/B:240 TYR criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
RSR57.pdb #!1/B TYR 240: phi -78.2, psi -19.6 trans  
Applying TYR rotamer (chi angles: -69.7 104.9) to RSR57.pdb #!1/B TYR 240  

> show #!18 models

> hide #!18 models

> undo

> redo

> select clear

> swapaa #!18/B:240 TYR criteria 3 rotLib Dunbrack retain false

Using Dunbrack library  
RSR57_Modified_with_Abeta46_GSM3.pdb #!18/B TYR 240: phi -78.2, psi -19.6
trans  
Applying TYR rotamer (chi angles: -69.7 79.4) to
RSR57_Modified_with_Abeta46_GSM3.pdb #!18/B TYR 240  

> close #1

> open /Users/u0154680/Documents/DailyWork/RSR57_complex_dockprep.pdb

Summary of feedback from opening
/Users/u0154680/Documents/DailyWork/RSR57_complex_dockprep.pdb  
---  
warnings | Cannot find LINK/SSBOND residue NAG (835 )  
Cannot find LINK/SSBOND residue NAG (842 )  
Cannot find LINK/SSBOND residue NAG (844 )  
Cannot find LINK/SSBOND residue NAG (801 )  
Cannot find LINK/SSBOND residue NAG (831 )  
9 messages similar to the above omitted  
  
Chain information for RSR57_complex_dockprep.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> select clear

> show #!1,18 atoms

> style #!1,18 stick

Changed 42225 atom styles  

> select ::name="GI9"

168 atoms, 180 bonds, 3 residues, 3 models selected  

> view sel

> hide #!1 models

> show #!1 models

> color #1 #3659c6ff

> select clear

> select ::name="GI9"

168 atoms, 180 bonds, 3 residues, 3 models selected  

> select sel : select ~sel

327354 atoms, 334065 bonds, 29 pseudobonds, 33267 residues, 40 models selected  

> hide sel & #!1,18 atoms

> hide sel & #!1,18 cartoons

> select clear

> select #1/B:177@HE1

1 atom, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel PHE rotLib Dunbrack

RSR57_complex_dockprep.pdb #1/B PHE 177: phi -69.6, psi -33.7 trans  
Changed 162 bond radii  


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac
      Model Identifier: Mac15,6
      Model Number: Z1AV001XFFN/A
      Chip: Unknown
      Total Number of Cores: 12 (6 performance and 6 efficiency)
      Memory: 36 GB
      System Firmware Version: 11881.1.1
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7 (23H124)
      Kernel Version: Darwin 23.6.0
      Time since boot: 35 days, 1 hour, 7 minutes

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 18
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP E243:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 12 months ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by Eric Pettersen, 12 months ago

Resolution: → duplicate
Status: assigned → closed
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