![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 19 months ago
Closed 19 months ago
#15033 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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)
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===== 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)
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How to cite UCSF ChimeraX
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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
Change History (2)
comment:1 by , 19 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Mitch,
--Eric