![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Last modified 12 months ago
#16243 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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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"name" : "libsystem_platform.dylib"
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"name" : "AppKit",
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"name" : "SkyLight"
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"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
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"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
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{
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"arch" : "x86_64",
"base" : 140703499493376,
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"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2732020,
"uuid" : "5f06f268-b51f-31fc-9dfc-ab1eced819c9",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703314452480,
"size" : 503796,
"uuid" : "acdb3afe-f896-313c-8d5b-2b2810639d29",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
],
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"uuid" : "f3bc3330-4c18-39e6-9f94-03e4df8c793e"
},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "8a79bac8f81cdd56f0d6765715b30eca1763d2a0",
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
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},
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},
{
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],
"experiments" : [
{
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}
]
},
"reportNotes" : [
"PC register does not match crashing frame (0x0 vs 0x7FF89B4BAA78)"
]
}
===== 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
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