id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15033 Crash in garbage collection alphataubio@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.2.1-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. i left chimerax open for a few hours while i was somewhere else. then when i started using chimerax again, i typed command ""open /Users/mitch/charmm/charmm-gui-1351004410/4pyg-3mM.psf coords /Users/mitch/Downloads/4pyg-3mM.dcd"" and it segfaulted Fatal Python error: Segmentation fault Current thread 0x00000002022142c0 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/md_crds/dcd/MDToolsMarch97/md_AtomGroup.py"", line 407 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/md_crds/read_psf.py"", line 84 in read_psf File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/md_crds/__init__.py"", line 39 in open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 484 in remember_data_format File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 513 in collated_open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 213 in provider_open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 131 in cmd_open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 55) {""app_name"":""ChimeraX"",""timestamp"":""2024-04-25 11:03:24.00 -0400"",""app_version"":""1.7.1"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.7.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.2.1 (22D68)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""813E23CA-554C-4219-8FBF-E6B59AA500D7""} { ""uptime"" : 370000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Macmini9,1"", ""coalitionID"" : 2961, ""osVersion"" : { ""train"" : ""macOS 13.2.1"", ""build"" : ""22D68"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-04-25 11:02:49.4001 -0400"", ""incident"" : ""813E23CA-554C-4219-8FBF-E6B59AA500D7"", ""pid"" : 34033, ""translated"" : true, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-04-22 03:30:04.5315 -0400"", ""procStartAbsTime"" : 2153111288874, ""procExitAbsTime"" : 9025894114480, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.1"",""CFBundleVersion"":""1.7.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""7566D2F4-E4BF-57AB-8EBB-F021CF50DEC1"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""41EDDFEC-52BA-2D61-985D-EFEDAC6DE678"", ""throttleTimeout"" : 2147483647, ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. Bytes before following region: 140723080216407\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffca5354000-7ffcafe20000 [170.8M] r-x\/r-x SM=COW ...t_id=60492197"", ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""vmregioninfo"" : ""0xa9 is not in any region. Bytes before following region: 140723080216407\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffca5354000-7ffcafe20000 [170.8M] r-x\/r-x SM=COW ...t_id=60492197"", ""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"" : [{""triggered"":true,""id"":1828679,""name"":""CrBrowserMain"",""threadState"":{""flavor"":""x86_THREAD_STATE"",""rbp"":{""value"":14757395258967641293},""r12"":{""value"":259},""rosetta"":{""tmp2"":{""value"":140703573283360},""tmp1"":{""value"":140705976215932},""tmp0"":{""value"":18446744073709551615}},""rbx"":{""value"":8670261952},""r8"":{""value"":11},""r15"":{""value"":22},""r10"":{""value"":8670261952},""rdx"":{""value"":0},""rdi"":{""value"":4531846256,""symbolLocation"":0,""symbol"":""faulthandler_handlers""},""r9"":{""value"":14757395258967641293},""r13"":{""value"":4513411073},""rflags"":{""value"":643},""rax"":{""value"":0},""rsp"":{""value"":2},""r11"":{""value"":105555615284748},""rcx"":{""value"":0},""r14"":{""value"":11},""rsi"":{""value"":4531475485}},""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":33322,""imageIndex"":1},{""imageOffset"":24443,""imageIndex"":2},{""imageOffset"":279680,""imageIndex"":3},{""imageOffset"":2590164,""symbol"":""faulthandler_fatal_error"",""symbolLocation"":388,""imageIndex"":4},{""imageOffset"":15389,""imageIndex"":5},{""imageOffset"":0,""imageIndex"":0},{""imageOffset"":111996,""imageIndex"":6}]},{""id"":1828686,""name"":""com.apple.rosetta.exceptionserver"",""frames"":[{""imageOffset"":17940,""imageIndex"":7},{""imageOffset"":66864,""imageIndex"":7},{""imageOffset"":73520,""imageIndex"":7}]},{""id"":1829456,""name"":""ThreadPoolServiceThread"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":44654,""imageIndex"":1},{""imageOffset"":66456106,""imageIndex"":8},{""imageOffset"":66455847,""imageIndex"":8},{""imageOffset"":65919580,""imageIndex"":8},{""imageOffset"":65624472,""imageIndex"":8},{""imageOffset"":66059960,""imageIndex"":8},{""imageOffset"":65958573,""imageIndex"":8},{""imageOffset"":66060362,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829458,""name"":""ThreadPoolBackgroundWorker"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":66009023,""imageIndex"":8},{""imageOffset"":66011756,""imageIndex"":8},{""imageOffset"":66010589,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829459,""name"":""Chrome_IOThread"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":44654,""imageIndex"":1},{""imageOffset"":66456106,""imageIndex"":8},{""imageOffset"":66455847,""imageIndex"":8},{""imageOffset"":65919580,""imageIndex"":8},{""imageOffset"":65624472,""imageIndex"":8},{""imageOffset"":66059960,""imageIndex"":8},{""imageOffset"":48386978,""imageIndex"":8},{""imageOffset"":66060362,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829460,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":66251759,""imageIndex"":8},{""imageOffset"":65421769,""imageIndex"":8},{""imageOffset"":65919580,""imageIndex"":8},{""imageOffset"":65624472,""imageIndex"":8},{""imageOffset"":66059960,""imageIndex"":8},{""imageOffset"":66060362,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829464,""name"":""CompositorTileWorker1"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":16666,""imageIndex"":1},{""imageOffset"":26593,""imageIndex"":2},{""imageOffset"":66219291,""imageIndex"":8},{""imageOffset"":100616493,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829465,""name"":""Chrome_InProcGpuThread"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":66251759,""imageIndex"":8},{""imageOffset"":65421769,""imageIndex"":8},{""imageOffset"":65919580,""imageIndex"":8},{""imageOffset"":65624472,""imageIndex"":8},{""imageOffset"":66059960,""imageIndex"":8},{""imageOffset"":66060362,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829466,""name"":""Chrome_ChildIOThread"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":44654,""imageIndex"":1},{""imageOffset"":66456106,""imageIndex"":8},{""imageOffset"":66455847,""imageIndex"":8},{""imageOffset"":65919580,""imageIndex"":8},{""imageOffset"":65624472,""imageIndex"":8},{""imageOffset"":66059960,""imageIndex"":8},{""imageOffset"":66060362,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829467,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":66251759,""imageIndex"":8},{""imageOffset"":65421769,""imageIndex"":8},{""imageOffset"":65919580,""imageIndex"":8},{""imageOffset"":65624472,""imageIndex"":8},{""imageOffset"":66059960,""imageIndex"":8},{""imageOffset"":66060362,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829468,""name"":""VizCompositorThread"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":65421672,""imageIndex"":8},{""imageOffset"":65919580,""imageIndex"":8},{""imageOffset"":65624472,""imageIndex"":8},{""imageOffset"":66059960,""imageIndex"":8},{""imageOffset"":66060362,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829476,""name"":""NetworkService"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":44654,""imageIndex"":1},{""imageOffset"":66456106,""imageIndex"":8},{""imageOffset"":66455847,""imageIndex"":8},{""imageOffset"":65919580,""imageIndex"":8},{""imageOffset"":65624472,""imageIndex"":8},{""imageOffset"":66059960,""imageIndex"":8},{""imageOffset"":66060362,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829477,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":66251759,""imageIndex"":8},{""imageOffset"":65421769,""imageIndex"":8},{""imageOffset"":65919580,""imageIndex"":8},{""imageOffset"":65624472,""imageIndex"":8},{""imageOffset"":66059960,""imageIndex"":8},{""imageOffset"":66060362,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829479,""name"":""ThreadPoolSingleThreadForegroundBlocking0"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":66009023,""imageIndex"":8},{""imageOffset"":66011756,""imageIndex"":8},{""imageOffset"":66010829,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829509,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":66251759,""imageIndex"":8},{""imageOffset"":65421769,""imageIndex"":8},{""imageOffset"":65919580,""imageIndex"":8},{""imageOffset"":65624472,""imageIndex"":8},{""imageOffset"":66059960,""imageIndex"":8},{""imageOffset"":66060362,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829545,""name"":""com.apple.NSEventThread"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":520203,""imageIndex"":9},{""imageOffset"":514660,""imageIndex"":9},{""imageOffset"":511615,""imageIndex"":9},{""imageOffset"":1700217,""imageIndex"":10},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829550,""name"":""MemoryInfra"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":66251759,""imageIndex"":8},{""imageOffset"":65421769,""imageIndex"":8},{""imageOffset"":65919580,""imageIndex"":8},{""imageOffset"":65624472,""imageIndex"":8},{""imageOffset"":66059960,""imageIndex"":8},{""imageOffset"":66060362,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1829551,""name"":""ThreadPoolSingleThreadSharedBackgroundBlocking1"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":66009023,""imageIndex"":8},{""imageOffset"":66011034,""imageIndex"":8},{""imageOffset"":66010637,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":1830846,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":66251759,""imageIndex"":8},{""imageOffset"":65421769,""imageIndex"":8},{""imageOffset"":65919580,""imageIndex"":8},{""imageOffset"":65624472,""imageIndex"":8},{""imageOffset"":66059960,""imageIndex"":8},{""imageOffset"":66060362,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":4320641,""name"":""ThreadPoolForegroundWorker"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":66009023,""imageIndex"":8},{""imageOffset"":66011756,""imageIndex"":8},{""imageOffset"":66010733,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":4421028,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]},{""id"":4421562,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]},{""id"":4421924,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]},{""id"":4422081,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]},{""id"":4422082,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]},{""id"":4423126,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]},{""id"":4423127,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]},{""id"":4423130,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]},{""id"":4424416,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]},{""id"":4424417,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]},{""id"":4424479,""name"":""ThreadPoolBackgroundWorker"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":66009023,""imageIndex"":8},{""imageOffset"":66011034,""imageIndex"":8},{""imageOffset"":66010589,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":4424663,""name"":""ThreadPoolForegroundWorker"",""frames"":[{""imageOffset"":140705976215976,""imageIndex"":0},{""imageOffset"":5570,""imageIndex"":1},{""imageOffset"":62980,""imageIndex"":1},{""imageOffset"":34357,""imageIndex"":1},{""imageOffset"":6312,""imageIndex"":1},{""imageOffset"":66252326,""imageIndex"":8},{""imageOffset"":66009023,""imageIndex"":8},{""imageOffset"":66011034,""imageIndex"":8},{""imageOffset"":66010733,""imageIndex"":8},{""imageOffset"":66222344,""imageIndex"":8},{""imageOffset"":25177,""imageIndex"":2},{""imageOffset"":7291,""imageIndex"":2}]},{""id"":4424665,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]},{""id"":4424666,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]},{""id"":4424668,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]},{""id"":4424670,""frames"":[{""imageOffset"":141436,""imageIndex"":7}]}], ""usedImages"" : [ { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703573250048, ""size"" : 237560, ""uuid"" : ""87ff381c-4d30-3087-bab7-a5a53d232c00"", ""path"" : ""\/usr\/lib\/system\/libsystem_kernel.dylib"", ""name"" : ""libsystem_kernel.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703573487616, ""size"" : 49144, ""uuid"" : ""3bd433d4-15bd-3add-a612-95e4d3b20719"", ""path"" : ""\/usr\/lib\/system\/libsystem_pthread.dylib"", ""name"" : ""libsystem_pthread.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703572234240, ""size"" : 561152, ""uuid"" : ""1aec5d1a-6e43-30f9-a9f2-11eb85d3e70c"", ""path"" : ""\/usr\/lib\/system\/libsystem_c.dylib"", ""name"" : ""libsystem_c.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4527448064, ""CFBundleShortVersionString"" : ""3.11.2, (c) 2001-2023 Python Software Foundation."", ""CFBundleIdentifier"" : ""org.python.python"", ""size"" : 4079616, ""uuid"" : ""24670b23-d78a-3eaa-bca8-22faf877f190"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python"", ""name"" : ""Python"", ""CFBundleVersion"" : ""3.11.2"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703573671936, ""size"" : 40952, ""uuid"" : ""04645919-7592-3a26-93b5-95663f983856"", ""path"" : ""\/usr\/lib\/system\/libsystem_platform.dylib"", ""name"" : ""libsystem_platform.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703571746816, ""size"" : 184320, ""uuid"" : ""d983a782-1a34-3466-9acb-94cbecd2f308"", ""path"" : ""\/usr\/lib\/system\/libsystem_malloc.dylib"", ""name"" : ""libsystem_malloc.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 140703125123072, ""size"" : 196608, ""uuid"" : ""f066db2c-ed38-3f37-8d21-81d15fa908fe"", ""path"" : ""\/usr\/libexec\/rosetta\/runtime"", ""name"" : ""runtime"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 5273124864, ""size"" : 165052416, ""uuid"" : ""4aa1de3e-464c-340c-ab61-bcd39bfc7658"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore"", ""name"" : ""QtWebEngineCore"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703573889024, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"", ""size"" : 4816896, ""uuid"" : ""be859dcd-e5ee-3aab-97e4-13231468695f"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"", ""CFBundleVersion"" : ""1953.300"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703625048064, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.AppKit"", ""size"" : 16814067, ""uuid"" : ""540cedfd-5a35-3f35-8953-dcb7c4834eb5"", ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"", ""name"" : ""AppKit"", ""CFBundleVersion"" : ""2299.40.118"" } ], ""sharedCache"" : { ""base"" : 140703569526784, ""size"" : 21474836480, ""uuid"" : ""4ca2b729-8206-3c63-badd-faa0225ab773"" }, ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6297d96be2c9387df974efa4"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 }, { ""rolloutId"" : ""645c2d2f9e69a025b0a37e29"", ""factorPackIds"" : { }, ""deploymentId"" : 240000003 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/mitch/charmm/charmm-gui-1351004410/4pyg-3mM.psf coords > /Users/mitch/Downloads/4pyg-3mM.dcd Summary of feedback from opening /Users/mitch/charmm/charmm- gui-1351004410/4pyg-3mM.psf --- notes | * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON APR, 19. 2024. JOB * READ PDB, MANIPULATE STRUCTURE IF NEEDED, AND GENERATE TOPOLOGY FILE * DATE: 4/19/24 3: 8:15 CREATED BY USER: apache Chain information for 4pyg-3mM.psf #1 --- Chain | Description A | No description available > coulombic The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /A ILE 112 /A ILE 136 /A ILE 167 /A ILE 175 /A ILE 178 /A ILE 189 /A ILE 192 /A ILE 195 /A ILE 255 /A ILE 260 /A ILE 293 /A ILE 313 /A ILE 323 /A ILE 331 /A ILE 379 /A ILE 405 /A ILE 416 /A ILE 421 /A ILE 426 /A ILE 439 /A ILE 477 /A ILE 495 /A ILE 519 /A ILE 546 /A ILE 561 /A ILE 572 /A ILE 589 /A ILE 591 /A ILE 593 /A ILE 638 /A ILE 683 /A ILE 684 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HSD (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmp9jlg_rjt/ante.in.mol2 -fi mol2 -o /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmp9jlg_rjt/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HSD) `` (HSD) `Welcome to antechamber 20.0: molecular input file processor.` (HSD) `` (HSD) `Info: Finished reading file (/var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmp9jlg_rjt/ante.in.mol2); atoms read (29), bonds read (29).` (HSD) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HSD) `` (HSD) `` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HSD) `Info: Total number of electrons: 112; net charge: 0` (HSD) `` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HSD) `` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (HSD) `` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (HSD) `` Charges for residue HSD determined Assigning partial charges to residue HSP (net charge +1) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpzkxcqfsw/ante.in.mol2 -fi mol2 -o /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpzkxcqfsw/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (HSP) `` (HSP) `Welcome to antechamber 20.0: molecular input file processor.` (HSP) `` (HSP) `Info: Finished reading file (/var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpzkxcqfsw/ante.in.mol2); atoms read (30), bonds read (30).` (HSP) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HSP) `` (HSP) `` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HSP) `Info: Total number of electrons: 112; net charge: 1` (HSP) `` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HSP) `` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (HSP) `` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (HSP) `` Charges for residue HSP determined Assigning partial charges to residue HSD+HSD+HSD+HSD+HSD+HSD (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpwo97claq/ante.in.mol2 -fi mol2 -o /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpwo97claq/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Welcome to antechamber 20.0: molecular input file processor.` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Finished reading file (/var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpwo97claq/ante.in.mol2); atoms read (112), bonds read (117).` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Total number of electrons: 466; net charge: 0` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HSD+HSD+HSD+HSD+HSD+HSD) `/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber: Fatal Error!` (HSD+HSD+HSD+HSD+HSD+HSD) `Cannot properly run ""/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/bin/amber20/bin/antechamber -i /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpwo97claq/ante.in.mol2 -fi mol2 -o /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpwo97claq/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Welcome to antechamber 20.0: molecular input file processor.` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Finished reading file (/var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpwo97claq/ante.in.mol2); atoms read (112), bonds read (117).` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Total number of electrons: 466; net charge: 0` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HSD+HSD+HSD+HSD+HSD+HSD) `/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber: Fatal Error!` (HSD+HSD+HSD+HSD+HSD+HSD) `Cannot properly run ""/Applications/ChimeraX-1.7.1.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 =169 | QMMM: *** Selected Hamiltonian *** | QMMM: AM1 | QMMM: *** Parameter sets in use *** | 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: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: O : 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 = 304 | QMMM: diag iterations used for timing = 2 | QMMM: | QMMM: Internal diag routine = 0.068446 seconds | QMMM: Dspev diag routine = 0.055884 seconds | QMMM: Dspevd diag routine = 0.043230 seconds | QMMM: Dspevx diag routine = 0.186916 seconds | QMMM: Dsyev diag routine = 0.058513 seconds | QMMM: Dsyevd diag routine = 0.044203 seconds | QMMM: Dsyevr diag routine = 0.047940 seconds | QMMM: | QMMM: Pseudo diag routine = 0.035490 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 N -18.9480 -29.4840 -11.6010 QMMM: 2 2 H -19.7620 -28.9150 -11.6880 QMMM: 3 3 C -18.0590 -29.3790 -12.7290 QMMM: 4 4 H -17.0610 -29.6870 -12.4560 QMMM: 5 5 C -18.5730 -30.0810 -13.9800 QMMM: 6 6 H -17.8450 -30.3660 -14.7690 QMMM: 7 7 H -19.3140 -29.4440 -14.5100 QMMM: 8 8 N -18.6200 -32.5970 -13.6460 QMMM: 9 9 H -17.8040 -32.6360 -13.0690 QMMM: 10 10 C -19.2440 -31.4230 -13.9550 QMMM: 11 11 C -19.4350 -33.5960 -13.8690 QMMM: 12 12 H -19.1210 -34.5810 -13.5240 QMMM: 13 13 N -20.5660 -33.2350 -14.3510 QMMM: 14 14 C -20.4350 -31.8670 -14.4230 QMMM: 15 15 H -21.3080 -31.3470 -14.8000 QMMM: 16 16 C -17.7690 -27.9440 -13.1660 QMMM: 17 17 O -18.6290 -27.0990 -12.9690 QMMM: 18 18 N -16.6200 -27.6630 -13.8940 QMMM: 19 19 H -15.9180 -28.3260 -14.1420 QMMM: 20 20 C -16.3150 -26.3240 -14.3950 QMMM: 21 21 H -17.2870 -25.8590 -14.4670 QMMM: 22 22 C -15.5120 -25.5980 -13.3120 QMMM: 23 23 H -14.8660 -26.3450 -12.8040 QMMM: 24 24 H -16.3130 -25.4290 -12.5610 QMMM: 25 25 N -13.6730 -23.7620 -13.2740 QMMM: 26 26 H -12.9410 -24.3350 -12.9070 QMMM: 27 27 C -14.9330 -24.2540 -13.6440 QMMM: 28 28 C -13.5900 -22.4700 -13.7490 QMMM: 29 29 H -12.7410 -21.8350 -13.4960 QMMM: 30 30 N -14.6780 -22.1010 -14.3790 QMMM: 31 31 C -15.5170 -23.1520 -14.2510 QMMM: 32 32 H -16.5600 -23.0070 -14.5030 QMMM: 33 33 C -15.5590 -26.3420 -15.7010 QMMM: 34 34 O -14.5030 -27.0180 -15.8110 QMMM: 35 35 N -16.0770 -25.6620 -16.7340 QMMM: 36 36 H -16.9120 -25.1610 -16.5200 QMMM: 37 37 C -15.5660 -25.7380 -18.0810 QMMM: 38 38 H -14.5620 -26.1310 -18.0150 QMMM: 39 39 C -16.5850 -26.5740 -18.8760 QMMM: 40 40 H -16.3030 -26.6710 -19.9460 QMMM: 41 41 H -17.6340 -26.2390 -18.7300 QMMM: 42 42 N -15.4220 -28.7210 -18.2350 QMMM: 43 43 H -14.4850 -28.4420 -18.4440 QMMM: 44 44 C -16.5470 -27.9560 -18.3680 QMMM: 45 45 C -15.7900 -29.9590 -17.8190 QMMM: 46 46 H -15.0610 -30.7580 -17.6790 QMMM: 47 47 N -17.1090 -30.0450 -17.7130 QMMM: 48 48 C -17.5570 -28.7700 -18.1040 QMMM: 49 49 H -18.6380 -28.7090 -18.0790 QMMM: 50 50 C -15.5170 -24.4500 -18.7860 QMMM: 51 51 O -14.8040 -24.2750 -19.7170 QMMM: 52 52 N -16.3340 -23.4490 -18.3260 QMMM: 53 53 H -16.9620 -23.6920 -17.5900 QMMM: 54 54 C -16.3810 -22.0710 -18.8310 QMMM: 55 55 H -16.6110 -22.1550 -19.8830 QMMM: 56 56 C -17.5270 -21.2800 -18.2070 QMMM: 57 57 H -17.5620 -21.3470 -17.0990 QMMM: 58 58 H -18.5000 -21.7080 -18.5310 QMMM: 59 59 N -17.3230 -18.7910 -17.5530 QMMM: 60 60 H -16.8750 -18.7860 -16.6590 QMMM: 61 61 C -17.4960 -19.7900 -18.4780 QMMM: 62 62 C -17.7680 -17.5990 -18.1520 QMMM: 63 63 H -17.8330 -16.6550 -17.6110 QMMM: 64 64 N -18.0400 -17.8370 -19.4480 QMMM: 65 65 C -17.8950 -19.2180 -19.6300 QMMM: 66 66 H -18.1790 -19.6460 -20.5830 QMMM: 67 67 C -15.0080 -21.3200 -18.6490 QMMM: 68 68 O -14.5780 -20.6000 -19.5980 QMMM: 69 69 N -14.3440 -21.6140 -17.5160 QMMM: 70 70 H -14.6890 -22.1420 -16.7440 QMMM: 71 71 C -12.9290 -21.3900 -17.4470 QMMM: 72 72 H -12.6410 -21.8450 -16.5110 QMMM: 73 73 C -12.0850 -22.1590 -18.4590 QMMM: 74 74 H -12.0880 -21.6190 -19.4300 QMMM: 75 75 H -12.6430 -23.0950 -18.6750 QMMM: 76 76 N -10.5200 -23.4280 -16.8560 QMMM: 77 77 H -11.2520 -24.0300 -16.5390 QMMM: 78 78 C -10.7100 -22.4940 -17.8280 QMMM: 79 79 C -9.2260 -23.7150 -16.7650 QMMM: 80 80 H -8.8040 -24.4240 -16.0520 QMMM: 81 81 N -8.5430 -22.8590 -17.5680 QMMM: 82 82 C -9.4690 -22.1260 -18.2450 QMMM: 83 83 H -9.1220 -21.4660 -19.0310 QMMM: 84 84 C -12.4980 -19.9150 -17.4660 QMMM: 85 85 O -11.4260 -19.5290 -17.9890 QMMM: 86 86 N -13.2910 -18.9650 -16.9800 QMMM: 87 87 H -14.2020 -19.1520 -16.6190 QMMM: 88 88 C -12.9490 -17.5550 -17.0210 QMMM: 89 89 H -12.0010 -17.3460 -17.4950 QMMM: 90 90 C -14.0520 -16.6310 -17.5480 QMMM: 91 91 H -13.9300 -15.5880 -17.1860 QMMM: 92 92 H -15.0930 -16.6970 -17.1650 QMMM: 93 93 N -14.4670 -17.7780 -19.9020 QMMM: 94 94 H -14.5390 -18.7580 -19.7130 QMMM: 95 95 C -14.0750 -16.7260 -19.1010 QMMM: 96 96 C -14.6670 -17.2990 -21.1120 QMMM: 97 97 H -15.0460 -17.9280 -21.9170 QMMM: 98 98 N -14.3930 -16.0010 -21.2420 QMMM: 99 99 C -14.0620 -15.6550 -19.9390 QMMM: 100 100 H -13.7200 -14.6400 -19.7790 QMMM: 101 101 C -12.8700 -17.2800 -15.4710 QMMM: 102 102 O -11.3580 37.2550 -42.5410 QMMM: 103 103 O 17.6910 -1.2420 49.9000 QMMM: 104 104 H -13.9230 -17.3450 -15.1960 QMMM: 105 105 H -11.3950 37.9450 -41.8740 QMMM: 106 106 H 17.7400 -0.2890 50.0060 QMMM: 107 107 C -18.5650 -30.0460 -10.4600 QMMM: 108 108 C -19.4610 -29.8470 -9.2660 QMMM: 109 109 H -19.5970 -28.7700 -9.0850 QMMM: 110 110 H -20.4390 -30.3120 -9.4610 QMMM: 111 111 H -19.0030 -30.3120 -8.3810 QMMM: 112 112 O -17.3860 -30.4580 -10.2660 -------------------------------------------------------------------------------- RESULTS -------------------------------------------------------------------------------- QMMM: ERROR! QMMM: Unable to achieve self consistency to the tolerances specified QMMM: No convergence in SCF after 1000 steps. QMMM: E = -0.3161E+07 DeltaE = -0.1340E+01 DeltaP = 0.1103E+01 QMMM: Smallest DeltaE = 0.3901E-02 DeltaP = 0.1181E+01 Step = 148 Failure running ANTECHAMBER for residue HSD+HSD+HSD+HSD+HSD+HSD Check reply log for details > style sphere Changed 10919 atom styles > show atoms > hide atoms > rainbow > coulombic The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /A ILE 112 /A ILE 136 /A ILE 167 /A ILE 175 /A ILE 178 /A ILE 189 /A ILE 192 /A ILE 195 /A ILE 255 /A ILE 260 /A ILE 293 /A ILE 313 /A ILE 323 /A ILE 331 /A ILE 379 /A ILE 405 /A ILE 416 /A ILE 421 /A ILE 426 /A ILE 439 /A ILE 477 /A ILE 495 /A ILE 519 /A ILE 546 /A ILE 561 /A ILE 572 /A ILE 589 /A ILE 591 /A ILE 593 /A ILE 638 /A ILE 683 /A ILE 684 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HSD (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpi4hxcod6/ante.in.mol2 -fi mol2 -o /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpi4hxcod6/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HSD) `` (HSD) `Welcome to antechamber 20.0: molecular input file processor.` (HSD) `` (HSD) `Info: Finished reading file (/var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpi4hxcod6/ante.in.mol2); atoms read (29), bonds read (29).` (HSD) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HSD) `` (HSD) `` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HSD) `Info: Total number of electrons: 112; net charge: 0` (HSD) `` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HSD) `` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (HSD) `` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (HSD) `` Charges for residue HSD determined Assigning partial charges to residue HSP (net charge +1) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpign9pgm5/ante.in.mol2 -fi mol2 -o /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpign9pgm5/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (HSP) `` (HSP) `Welcome to antechamber 20.0: molecular input file processor.` (HSP) `` (HSP) `Info: Finished reading file (/var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpign9pgm5/ante.in.mol2); atoms read (30), bonds read (30).` (HSP) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HSP) `` (HSP) `` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HSP) `Info: Total number of electrons: 112; net charge: 1` (HSP) `` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HSP) `` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (HSP) `` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (HSP) `` Charges for residue HSP determined Assigning partial charges to residue HSD+HSD+HSD+HSD+HSD+HSD (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmprb366vkt/ante.in.mol2 -fi mol2 -o /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmprb366vkt/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Welcome to antechamber 20.0: molecular input file processor.` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Finished reading file (/var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmprb366vkt/ante.in.mol2); atoms read (112), bonds read (117).` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Total number of electrons: 466; net charge: 0` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HSD+HSD+HSD+HSD+HSD+HSD) `/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber: Fatal Error!` (HSD+HSD+HSD+HSD+HSD+HSD) `Cannot properly run ""/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/bin/amber20/bin/antechamber -i /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmprb366vkt/ante.in.mol2 -fi mol2 -o /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmprb366vkt/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Welcome to antechamber 20.0: molecular input file processor.` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Finished reading file (/var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmprb366vkt/ante.in.mol2); atoms read (112), bonds read (117).` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Total number of electrons: 466; net charge: 0` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HSD+HSD+HSD+HSD+HSD+HSD) `/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber: Fatal Error!` (HSD+HSD+HSD+HSD+HSD+HSD) `Cannot properly run ""/Applications/ChimeraX-1.7.1.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 =169 | QMMM: *** Selected Hamiltonian *** | QMMM: AM1 | QMMM: *** Parameter sets in use *** | 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: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: O : 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 = 304 | QMMM: diag iterations used for timing = 2 | QMMM: | QMMM: Internal diag routine = 0.069093 seconds | QMMM: Dspev diag routine = 0.056412 seconds | QMMM: Dspevd diag routine = 0.043989 seconds | QMMM: Dspevx diag routine = 0.189637 seconds | QMMM: Dsyev diag routine = 0.058936 seconds | QMMM: Dsyevd diag routine = 0.044277 seconds | QMMM: Dsyevr diag routine = 0.047984 seconds | QMMM: | QMMM: Pseudo diag routine = 0.035549 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 N -22.7560 -27.7710 -10.2850 QMMM: 2 2 H -23.7310 -27.6060 -10.1530 QMMM: 3 3 C -22.1800 -27.8330 -11.6350 QMMM: 4 4 H -21.2860 -28.4390 -11.6340 QMMM: 5 5 C -23.0580 -28.5800 -12.6860 QMMM: 6 6 H -22.7670 -28.2390 -13.7030 QMMM: 7 7 H -24.1190 -28.3070 -12.5000 QMMM: 8 8 N -22.0710 -30.9410 -13.1230 QMMM: 9 9 H -21.2440 -30.6650 -13.6120 QMMM: 10 10 C -23.0240 -30.0920 -12.5610 QMMM: 11 11 C -22.3210 -32.1640 -12.6480 QMMM: 12 12 H -21.6910 -33.0240 -12.8730 QMMM: 13 13 N -23.3560 -32.2240 -11.8700 QMMM: 14 14 C -23.8730 -30.9030 -11.8550 QMMM: 15 15 H -24.6990 -30.7100 -11.1810 QMMM: 16 16 C -21.8710 -26.4110 -12.1240 QMMM: 17 17 O -22.7750 -25.6140 -12.3090 QMMM: 18 18 N -20.6210 -26.1210 -12.4250 QMMM: 19 19 H -19.8970 -26.7840 -12.2520 QMMM: 20 20 C -20.2190 -24.9570 -13.1290 QMMM: 21 21 H -21.0480 -24.5470 -13.6870 QMMM: 22 22 C -19.6680 -23.8440 -12.1170 QMMM: 23 23 H -18.9110 -24.2330 -11.4020 QMMM: 24 24 H -20.5390 -23.4010 -11.5890 QMMM: 25 25 N -17.4730 -22.4970 -12.3400 QMMM: 26 26 H -16.9420 -22.9310 -11.6110 QMMM: 27 27 C -18.7960 -22.7300 -12.7120 QMMM: 28 28 C -17.0380 -21.4780 -13.1850 QMMM: 29 29 H -16.0310 -21.0630 -13.1680 QMMM: 30 30 N -17.9950 -21.0200 -14.0030 QMMM: 31 31 C -19.1140 -21.8270 -13.7060 QMMM: 32 32 H -20.0660 -21.7570 -14.2190 QMMM: 33 33 C -19.2150 -25.2650 -14.1470 QMMM: 34 34 O -18.1550 -25.7800 -13.7690 QMMM: 35 35 N -19.4620 -24.8860 -15.4680 QMMM: 36 36 H -20.2930 -24.4250 -15.7680 QMMM: 37 37 C -18.5100 -25.2630 -16.5260 QMMM: 38 38 H -17.5210 -25.3800 -16.1070 QMMM: 39 39 C -19.0000 -26.5350 -17.2390 QMMM: 40 40 H -18.2260 -26.8500 -17.9710 QMMM: 41 41 H -19.9620 -26.2100 -17.6910 QMMM: 42 42 N -18.2280 -28.3290 -15.6650 QMMM: 43 43 H -17.2520 -28.1140 -15.7010 QMMM: 44 44 C -19.2880 -27.7090 -16.3260 QMMM: 45 45 C -18.8080 -29.2510 -14.9080 QMMM: 46 46 H -18.2840 -30.0260 -14.3490 QMMM: 47 47 N -20.1680 -29.2700 -15.0140 QMMM: 48 48 C -20.4600 -28.3000 -15.9280 QMMM: 49 49 H -21.4710 -27.9180 -15.9970 QMMM: 50 50 C -18.3360 -24.1430 -17.4920 QMMM: 51 51 O -17.7900 -24.3280 -18.5700 QMMM: 52 52 N -18.8870 -22.9150 -17.1510 QMMM: 53 53 H -19.6260 -22.8170 -16.4900 QMMM: 54 54 C -18.6670 -21.7470 -17.9250 QMMM: 55 55 H -18.7520 -21.9180 -18.9880 QMMM: 56 56 C -19.8400 -20.7390 -17.6650 QMMM: 57 57 H -19.8850 -20.5240 -16.5760 QMMM: 58 58 H -20.8480 -21.1130 -17.9460 QMMM: 59 59 N -20.1510 -18.2480 -17.6510 QMMM: 60 60 H -20.2140 -18.1300 -16.6600 QMMM: 61 61 C -19.7450 -19.3870 -18.3340 QMMM: 62 62 C -20.4500 -17.3510 -18.5730 QMMM: 63 63 H -20.5360 -16.2750 -18.4200 QMMM: 64 64 N -20.2690 -17.7620 -19.8100 QMMM: 65 65 C -19.8440 -19.0390 -19.6370 QMMM: 66 66 H -19.4600 -19.6550 -20.4410 QMMM: 67 67 C -17.2660 -21.1790 -17.7290 QMMM: 68 68 O -16.7350 -20.7480 -18.7490 QMMM: 69 69 N -16.6040 -21.2210 -16.5360 QMMM: 70 70 H -17.1130 -21.5520 -15.7450 QMMM: 71 71 C -15.2620 -20.7760 -16.2450 QMMM: 72 72 H -15.1210 -21.1200 -15.2310 QMMM: 73 73 C -14.2330 -21.6090 -17.1690 QMMM: 74 74 H -14.2510 -21.1310 -18.1720 QMMM: 75 75 H -14.6040 -22.6540 -17.2370 QMMM: 76 76 N -12.4900 -21.9780 -15.2200 QMMM: 77 77 H -13.1430 -22.3310 -14.5500 QMMM: 78 78 C -12.8520 -21.6080 -16.5010 QMMM: 79 79 C -11.1480 -21.7680 -15.1210 QMMM: 80 80 H -10.5460 -21.8550 -14.2160 QMMM: 81 81 N -10.6390 -21.2540 -16.1980 QMMM: 82 82 C -11.6890 -21.1720 -17.1120 QMMM: 83 83 H -11.5070 -20.8410 -18.1280 QMMM: 84 84 C -15.0230 -19.2510 -16.2510 QMMM: 85 85 O -13.9050 -18.8820 -16.6120 QMMM: 86 86 N -15.9570 -18.3580 -15.9200 QMMM: 87 87 H -16.8250 -18.7390 -15.6110 QMMM: 88 88 C -15.7870 -16.9130 -15.7410 QMMM: 89 89 H -14.7800 -16.6320 -16.0120 QMMM: 90 90 C -16.7840 -16.0560 -16.6560 QMMM: 91 91 H -16.6240 -14.9870 -16.3990 QMMM: 92 92 H -17.8490 -16.2760 -16.4330 QMMM: 93 93 N -17.0720 -17.0190 -18.9020 QMMM: 94 94 H -17.9580 -17.3540 -18.5830 QMMM: 95 95 C -16.4120 -16.1390 -18.1040 QMMM: 96 96 C -16.5990 -16.8870 -20.1400 QMMM: 97 97 H -16.9970 -17.3830 -21.0260 QMMM: 98 98 N -15.5480 -16.0060 -20.1530 QMMM: 99 99 C -15.4720 -15.5230 -18.8860 QMMM: 100 100 H -14.7680 -14.7310 -18.6620 QMMM: 101 101 C -16.0500 -16.4370 -14.2750 QMMM: 102 102 O -12.2340 37.3870 -41.8540 QMMM: 103 103 O 17.6890 -2.6160 48.6040 QMMM: 104 104 H -17.1010 -16.6200 -14.0520 QMMM: 105 105 H -12.3240 38.0870 -41.2040 QMMM: 106 106 H 17.7560 -1.6670 48.7300 QMMM: 107 107 C -22.0640 -28.1260 -9.1690 QMMM: 108 108 C -22.8250 -28.1100 -7.7380 QMMM: 109 109 H -22.9920 -27.0700 -7.4220 QMMM: 110 110 H -23.7920 -28.6250 -7.8310 QMMM: 111 111 H -22.2060 -28.6250 -6.9880 QMMM: 112 112 O -20.8500 -28.3590 -9.2290 -------------------------------------------------------------------------------- RESULTS -------------------------------------------------------------------------------- QMMM: ERROR! QMMM: Unable to achieve self consistency to the tolerances specified QMMM: No convergence in SCF after 1000 steps. QMMM: E = -0.3154E+07 DeltaE = -0.5288E+01 DeltaP = 0.1049E+01 QMMM: Smallest DeltaE = -0.7994E-02 DeltaP = 0.1128E+01 Step = 287 Failure running ANTECHAMBER for residue HSD+HSD+HSD+HSD+HSD+HSD Check reply log for details > show atoms > select add #1 10919 atoms, 11033 bonds, 705 residues, 1 model selected > close > open /Users/mitch/charmm/charmm-gui-1351004410/4pyg-3mM.psf coords > /Users/mitch/Downloads/4pyg-3mM.dcd Summary of feedback from opening /Users/mitch/charmm/charmm- gui-1351004410/4pyg-3mM.psf --- notes | * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON APR, 19. 2024. JOB * READ PDB, MANIPULATE STRUCTURE IF NEEDED, AND GENERATE TOPOLOGY FILE * DATE: 4/19/24 3: 8:15 CREATED BY USER: apache Chain information for 4pyg-3mM.psf #1 --- Chain | Description A | No description available > close > open /Users/mitch/charmm/charmm-gui-1351004410/4pyg-3mM.psf coords > /Users/mitch/Downloads/4pyg-3mM.dcd Summary of feedback from opening /Users/mitch/charmm/charmm- gui-1351004410/4pyg-3mM.psf --- notes | * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON APR, 19. 2024. JOB * READ PDB, MANIPULATE STRUCTURE IF NEEDED, AND GENERATE TOPOLOGY FILE * DATE: 4/19/24 3: 8:15 CREATED BY USER: apache Chain information for 4pyg-3mM.psf #1 --- Chain | Description A | No description available > rainbow > coulombic The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /A ILE 112 /A ILE 136 /A ILE 167 /A ILE 175 /A ILE 178 /A ILE 189 /A ILE 192 /A ILE 195 /A ILE 255 /A ILE 260 /A ILE 293 /A ILE 313 /A ILE 323 /A ILE 331 /A ILE 379 /A ILE 405 /A ILE 416 /A ILE 421 /A ILE 426 /A ILE 439 /A ILE 477 /A ILE 495 /A ILE 519 /A ILE 546 /A ILE 561 /A ILE 572 /A ILE 589 /A ILE 591 /A ILE 593 /A ILE 638 /A ILE 683 /A ILE 684 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HSD (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpv8oxnq_m/ante.in.mol2 -fi mol2 -o /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpv8oxnq_m/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HSD) `` (HSD) `Welcome to antechamber 20.0: molecular input file processor.` (HSD) `` (HSD) `Info: Finished reading file (/var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpv8oxnq_m/ante.in.mol2); atoms read (29), bonds read (29).` (HSD) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HSD) `` (HSD) `` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HSD) `Info: Total number of electrons: 112; net charge: 0` (HSD) `` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HSD) `` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (HSD) `` (HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (HSD) `` Charges for residue HSD determined Assigning partial charges to residue HSP (net charge +1) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpzetb3ddt/ante.in.mol2 -fi mol2 -o /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpzetb3ddt/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (HSP) `` (HSP) `Welcome to antechamber 20.0: molecular input file processor.` (HSP) `` (HSP) `Info: Finished reading file (/var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpzetb3ddt/ante.in.mol2); atoms read (30), bonds read (30).` (HSP) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HSP) `` (HSP) `` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HSP) `Info: Total number of electrons: 112; net charge: 1` (HSP) `` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HSP) `` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (HSP) `` (HSP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (HSP) `` Charges for residue HSP determined Assigning partial charges to residue HSD+HSD+HSD+HSD+HSD+HSD (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpz9dlpxw_/ante.in.mol2 -fi mol2 -o /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpz9dlpxw_/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Welcome to antechamber 20.0: molecular input file processor.` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Finished reading file (/var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpz9dlpxw_/ante.in.mol2); atoms read (112), bonds read (117).` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Total number of electrons: 466; net charge: 0` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HSD+HSD+HSD+HSD+HSD+HSD) `/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber: Fatal Error!` (HSD+HSD+HSD+HSD+HSD+HSD) `Cannot properly run ""/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/bin/amber20/bin/antechamber -i /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpz9dlpxw_/ante.in.mol2 -fi mol2 -o /var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpz9dlpxw_/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Welcome to antechamber 20.0: molecular input file processor.` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Finished reading file (/var/folders/w6/v73x419x183g9_q5md_kgprh0000gn/T/tmpz9dlpxw_/ante.in.mol2); atoms read (112), bonds read (117).` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HSD+HSD+HSD+HSD+HSD+HSD) `Info: Total number of electrons: 466; net charge: 0` (HSD+HSD+HSD+HSD+HSD+HSD) `` (HSD+HSD+HSD+HSD+HSD+HSD) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HSD+HSD+HSD+HSD+HSD+HSD) `/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber: Fatal Error!` (HSD+HSD+HSD+HSD+HSD+HSD) `Cannot properly run ""/Applications/ChimeraX-1.7.1.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 =169 | QMMM: *** Selected Hamiltonian *** | QMMM: AM1 | QMMM: *** Parameter sets in use *** | 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: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: O : 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 = 304 | QMMM: diag iterations used for timing = 2 | QMMM: | QMMM: Internal diag routine = 0.068462 seconds | QMMM: Dspev diag routine = 0.055955 seconds | QMMM: Dspevd diag routine = 0.043205 seconds | QMMM: Dspevx diag routine = 0.188061 seconds | QMMM: Dsyev diag routine = 0.058717 seconds | QMMM: Dsyevd diag routine = 0.044344 seconds | QMMM: Dsyevr diag routine = 0.047976 seconds | QMMM: | QMMM: Pseudo diag routine = 0.035593 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 N -13.1030 -34.6350 -11.2610 QMMM: 2 2 H -14.0290 -34.2930 -11.1210 QMMM: 3 3 C -12.6490 -34.6700 -12.6430 QMMM: 4 4 H -11.5770 -34.7950 -12.6070 QMMM: 5 5 C -13.2920 -35.8180 -13.3900 QMMM: 6 6 H -13.0550 -35.7830 -14.4740 QMMM: 7 7 H -14.3930 -35.8440 -13.2470 QMMM: 8 8 N -11.5660 -37.6520 -12.8600 QMMM: 9 9 H -10.7950 -37.1900 -13.2970 QMMM: 10 10 C -12.8930 -37.1710 -12.8500 QMMM: 11 11 C -11.5250 -38.9340 -12.4040 QMMM: 12 12 H -10.5870 -39.4700 -12.2610 QMMM: 13 13 N -12.7800 -39.3520 -12.0650 QMMM: 14 14 C -13.6040 -38.2200 -12.4000 QMMM: 15 15 H -14.5500 -38.2780 -11.8750 QMMM: 16 16 C -13.0750 -33.3890 -13.3580 QMMM: 17 17 O -14.2040 -33.0560 -13.4650 QMMM: 18 18 N -12.1160 -32.6210 -13.8670 QMMM: 19 19 H -11.2100 -33.0380 -13.8720 QMMM: 20 20 C -12.2940 -31.3170 -14.4830 QMMM: 21 21 H -13.3080 -30.9940 -14.2980 QMMM: 22 22 C -11.3880 -30.3290 -13.6860 QMMM: 23 23 H -10.4120 -30.8080 -13.4570 QMMM: 24 24 H -11.9040 -30.1900 -12.7120 QMMM: 25 25 N -10.1340 -28.1980 -14.3070 QMMM: 26 26 H -9.2080 -28.5570 -14.1840 QMMM: 27 27 C -11.2900 -28.9420 -14.2770 QMMM: 28 28 C -10.4950 -27.1000 -15.0440 QMMM: 29 29 H -9.7850 -26.2800 -15.1510 QMMM: 30 30 N -11.7900 -27.0220 -15.2610 QMMM: 31 31 C -12.2930 -28.2490 -14.8750 QMMM: 32 32 H -13.3380 -28.4950 -15.0130 QMMM: 33 33 C -12.2150 -31.1660 -16.0070 QMMM: 34 34 O -11.2380 -31.6010 -16.6460 QMMM: 35 35 N -13.2520 -30.5740 -16.6520 QMMM: 36 36 H -14.0570 -30.2900 -16.1380 QMMM: 37 37 C -13.4240 -30.6670 -18.0910 QMMM: 38 38 H -12.4370 -30.7120 -18.5260 QMMM: 39 39 C -14.4720 -31.7960 -18.5500 QMMM: 40 40 H -14.4320 -31.9790 -19.6450 QMMM: 41 41 H -15.4490 -31.4280 -18.1690 QMMM: 42 42 N -13.8800 -34.2910 -18.5410 QMMM: 43 43 H -13.5540 -34.1720 -19.4790 QMMM: 44 44 C -14.3040 -33.1550 -17.9100 QMMM: 45 45 C -14.1670 -35.2920 -17.7250 QMMM: 46 46 H -14.1080 -36.3620 -17.9240 QMMM: 47 47 N -14.7740 -34.9800 -16.6120 QMMM: 48 48 C -14.8480 -33.5900 -16.7520 QMMM: 49 49 H -15.2960 -33.0120 -15.9530 QMMM: 50 50 C -13.9930 -29.3880 -18.6410 QMMM: 51 51 O -14.5470 -29.4550 -19.7570 QMMM: 52 52 N -13.9360 -28.3370 -17.8740 QMMM: 53 53 H -13.6350 -28.4450 -16.9300 QMMM: 54 54 C -14.4550 -27.0560 -18.2520 QMMM: 55 55 H -15.0990 -27.2320 -19.1010 QMMM: 56 56 C -15.3790 -26.4620 -17.0710 QMMM: 57 57 H -14.9690 -26.4160 -16.0390 QMMM: 58 58 H -16.1980 -27.2110 -17.0990 QMMM: 59 59 N -15.4970 -23.8960 -16.7140 QMMM: 60 60 H -14.9860 -23.9600 -15.8570 QMMM: 61 61 C -15.9140 -24.9910 -17.3890 QMMM: 62 62 C -16.0030 -22.8000 -17.3760 QMMM: 63 63 H -15.7980 -21.7910 -17.0190 QMMM: 64 64 N -16.6480 -23.1680 -18.4490 QMMM: 65 65 C -16.6350 -24.5130 -18.4620 QMMM: 66 66 H -17.1810 -25.0600 -19.2210 QMMM: 67 67 C -13.3960 -26.0100 -18.4980 QMMM: 68 68 O -13.6320 -25.1150 -19.2230 QMMM: 69 69 N -12.1490 -26.2100 -18.0070 QMMM: 70 70 H -11.9680 -26.9170 -17.3270 QMMM: 71 71 C -10.9600 -25.5490 -18.4910 QMMM: 72 72 H -10.2670 -26.0210 -17.8100 QMMM: 73 73 C -10.5690 -25.9130 -19.9700 QMMM: 74 74 H -11.3130 -25.3860 -20.6030 QMMM: 75 75 H -10.8130 -26.9830 -20.1420 QMMM: 76 76 N -8.0000 -26.0210 -19.5820 QMMM: 77 77 H -7.9580 -26.7760 -18.9280 QMMM: 78 78 C -9.1340 -25.6970 -20.3660 QMMM: 79 79 C -6.9460 -25.5640 -20.3120 QMMM: 80 80 H -5.9700 -25.6730 -19.8370 QMMM: 81 81 N -7.2710 -25.0330 -21.4220 QMMM: 82 82 C -8.6740 -25.1880 -21.4470 QMMM: 83 83 H -9.0730 -24.9800 -22.4320 QMMM: 84 84 C -10.8370 -24.0000 -18.2100 QMMM: 85 85 O -10.2290 -23.2680 -18.9770 QMMM: 86 86 N -11.4140 -23.5060 -17.1010 QMMM: 87 87 H -11.8510 -24.1280 -16.4560 QMMM: 88 88 C -11.5120 -22.1570 -16.7790 QMMM: 89 89 H -10.6220 -21.6900 -17.1740 QMMM: 90 90 C -12.8280 -21.5900 -17.1570 QMMM: 91 91 H -12.8640 -20.5420 -16.7890 QMMM: 92 92 H -13.6560 -22.2060 -16.7460 QMMM: 93 93 N -13.6470 -22.3980 -19.4430 QMMM: 94 94 H -13.7260 -23.3380 -19.1130 QMMM: 95 95 C -12.9980 -21.4820 -18.6380 QMMM: 96 96 C -13.6550 -21.8790 -20.6910 QMMM: 97 97 H -14.1880 -22.3620 -21.5100 QMMM: 98 98 N -13.0500 -20.6590 -20.7260 QMMM: 99 99 C -12.6290 -20.4480 -19.4310 QMMM: 100 100 H -12.1460 -19.5010 -19.2260 QMMM: 101 101 C -11.2050 -21.9530 -15.2480 QMMM: 102 102 O -11.8540 36.2680 -42.5300 QMMM: 103 103 O 17.6780 -0.8740 49.4610 QMMM: 104 104 H -12.2440 -21.9400 -14.9210 QMMM: 105 105 H -11.8380 36.9430 -41.8470 QMMM: 106 106 H 17.6980 0.0850 49.5060 QMMM: 107 107 C -12.3230 -34.7820 -10.1930 QMMM: 108 108 C -13.0190 -34.6700 -8.8350 QMMM: 109 109 H -13.1520 -33.6090 -8.5760 QMMM: 110 110 H -12.4040 -35.1610 -8.0660 QMMM: 111 111 H -14.0020 -35.1610 -8.8850 QMMM: 112 112 O -11.1810 -35.1080 -10.2370 -------------------------------------------------------------------------------- RESULTS -------------------------------------------------------------------------------- QMMM: ERROR! QMMM: Unable to achieve self consistency to the tolerances specified QMMM: No convergence in SCF after 1000 steps. QMMM: E = -0.3152E+07 DeltaE = -0.8827E+00 DeltaP = 0.1037E+01 QMMM: Smallest DeltaE = 0.1222E+00 DeltaP = 0.1023E+01 Step = 903 Failure running ANTECHAMBER for residue HSD+HSD+HSD+HSD+HSD+HSD Check reply log for details > style stick Changed 10919 atom styles > show atoms > select Cl Nothing selected > select ligand Nothing selected > close > open /Users/mitch/charmm/charmm-gui-1351004410/4pyg-3mM.psf coords > /Users/mitch/Downloads/4pyg-3mM.dcd ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac mini Model Identifier: Macmini9,1 Model Number: G12N1LL/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8419.80.7 OS Loader Version: 8419.80.7 Software: System Software Overview: System Version: macOS 13.2.1 (22D68) Kernel Version: Darwin 22.3.0 Time since boot: 4 days, 15 hours, 45 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL U3011: Resolution: 2560 x 1600 UI Looks like: 2560 x 1600 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 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: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 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: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX