Opened 7 months ago

Last modified 7 months ago

#17232 assigned defect

ORCA output: could not convert string to float

Reported by: kst61@… Owned by: Tony Schaefer
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Attempted to open a S1 optimization run of an ORCA output file. Windows 11. ORCA version 5.0.3

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

QWindowsWindow::setGeometry: Unable to set geometry 1058x1096+671+166 (frame:
1076x1143+662+128) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1056x1088+672+173 (frame:
1074x1135+663+135) margins: 9, 38, 9, 9 minimum size: 840x877 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=1068, y=1143)))  

> toolshed show

QWindowsWindow::setGeometry: Unable to set geometry 1058x1096+671+166 (frame:
1076x1143+662+128) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1056x1088+672+173 (frame:
1074x1135+663+135) margins: 9, 38, 9, 9 minimum size: 840x877 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=1068, y=1143)))  

Downloading bundle SEQCROW-1.8.18-py3-none-any.whl  
Installed SEQCROW (1.8.18)  

> ui tool show "Build QM Input"

settings migrated from version 2  

QWindowsWindow::setGeometry: Unable to set geometry 1330x633+535+398 (frame:
1348x680+526+360) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1328x625+536+405 (frame:
1346x672+527+367) margins: 9, 38, 9, 9 minimum size: 417x375 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=539, y=516)))  

> ui mousemode right distance

[Repeated 1 time(s)]

> ui mousemode right select

> open "H:/My Drive/Crespo/Rhodanines/1/ACN/1_gs_opt_freq/1-acn-opt-freq.out"

Summary of feedback from opening H:/My
Drive/Crespo/Rhodanines/1/ACN/1_gs_opt_freq/1-acn-opt-freq.out  
---  
note | 1-acn-opt-freq.out has 0 imaginary harmonic vibrational modes  
  
Opened 1-acn-opt-freq.out as an ORCA output file  

QWindowsWindow::setGeometry: Unable to set geometry 553x411+924+509 (frame:
571x458+915+471) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 551x403+925+516 (frame: 569x450+916+478)
margins: 9, 38, 9, 9 minimum size: 442x329 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=571, y=458)))  

> open "H:/My
> Drive/Crespo/Rhodanines/GS_reaction_pathways_Z_E/5/8_vac_optts_wb97M-V/8_vac_optts_wB97M-V.out"

Summary of feedback from opening H:/My
Drive/Crespo/Rhodanines/GS_reaction_pathways_Z_E/5/8_vac_optts_wb97M-V/8_vac_optts_wB97M-V.out  
---  
notes | 8_vac_optts_wB97M-V.out has 2 imaginary harmonic vibrational modes  
889.99i  
41.66i  
  
  
Opened 8_vac_optts_wB97M-V.out as an ORCA output file  

QWindowsWindow::setGeometry: Unable to set geometry 553x411+924+509 (frame:
571x458+915+471) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 551x403+925+516 (frame: 569x450+916+478)
margins: 9, 38, 9, 9 minimum size: 442x329 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=571, y=458)))  

> close #1

> close

> open "H:/My
> Drive/Crespo/Rhodanines/GS_reaction_pathways_Z_E/5/2-vacuum_xtb/1-nebts_xtb/output/1-nebts_xtb.out"

Opened 1-nebts_xtb.out as an ORCA output file  

QWindowsWindow::setGeometry: Unable to set geometry 553x411+924+509 (frame:
571x458+915+471) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 551x403+925+516 (frame: 569x450+916+478)
margins: 9, 38, 9, 9 minimum size: 442x329 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=571, y=458)))  

> select clear

> close

> open "H:/My
> Drive/Crespo/Rhodanines/GS_reaction_pathways_Z_E/5/2-vacuum_xtb/1-nebts_xtb/output/1-nebts_xtb_MEP_trj.xyz"

opened 1-nebts_xtb_MEP_trj.xyz as an XYZ coordinate file movie  

QWindowsWindow::setGeometry: Unable to set geometry 553x449+924+490 (frame:
571x496+915+452) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 551x441+925+497 (frame: 569x488+916+459)
margins: 9, 38, 9, 9 minimum size: 442x359 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=571, y=496)))  

> open "H:/My
> Drive/Crespo/Rhodanines/5S/Water/6_S1_opt_freq/5S_water_S1_opt_freq_soc.out"

Summary of feedback from opening H:/My
Drive/Crespo/Rhodanines/5S/Water/6_S1_opt_freq/5S_water_S1_opt_freq_soc.out  
---  
error | unable to open 5S_water_S1_opt_freq_soc.out as a ORCA output file  
warnings | WARNING AaronTools.fileIO.FileReader.read_orca_out   
an error occured while reading the ORCA output file  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR ***  
  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR ***  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR ***  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
  
================================================================================  
NAME = S1_opt_freq_soc.inp  
| 1> # Excite to get 8 singlet excited states and optimize S1  
| 2>  
| 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2  
CPCM(water)  
| 4>  
| 5> %maxcore 6000  
| 6>  
| 7> %base "5S_S1_opt_freq_1" #WATER!!!!  
| 8>  
| 9> %cpcm  
| 10> num_leb 302  
| 11> end  
| 12>  
| 13> %scf  
| 14> maxiter 300  
| 15> end  
| 16>  
| 17> %geom  
| 18> maxiter 300  
| 19> end  
| 20>  
| 21> %pal  
| 22> nprocs 16  
| 23> end  
| 24>  
| 25> %tddft  
| 26> NROOTS 8  
| 27>  
| 28> # Optimize S1  
| 29> IROOT 1  
| 30>  
| 31> # Which type of states for IROOT? singlet.  
  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR ***  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
  
================================================================================  
NAME = S1_opt_freq_soc.inp  
| 1> # Excite to get 8 singlet excited states and optimize S1  
| 2>  
| 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2  
CPCM(water)  
| 4>  
| 5> %maxcore 6000  
| 6>  
| 7> %base "5S_S1_opt_freq_1" #WATER!!!!  
| 8>  
| 9> %cpcm  
| 10> num_leb 302  
| 11> end  
| 12>  
| 13> %scf  
| 14> maxiter 300  
| 15> end  
| 16>  
| 17> %geom  
| 18> maxiter 300  
| 19> end  
| 20>  
| 21> %pal  
| 22> nprocs 16  
| 23> end  
| 24>  
| 25> %tddft  
| 26> NROOTS 8  
| 27>  
| 28> # Optimize S1  
| 29> IROOT 1  
| 30>  
| 31> # Which type of states for IROOT? singlet.  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 54, in event  
if self.handle_drag_and_drop(event):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 124, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py",
line 731, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py",
line 2117, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\\__init__.py", line 596, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\io.py", line 46, in open_aarontools  
raise e  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\io.py", line 33, in open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\fileIO.py", line 1630, in __init__  
self.read_orca_out(f, get_all, just_geom, log=None)  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\fileIO.py", line 3189, in read_orca_out  
raise e  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\fileIO.py", line 3031, in read_orca_out  
self.other["uv_vis"] = ValenceExcitations(s, orca_version=orca_version,
style="orca")  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 1429, in __init__  
super().__init__(*args, **kwargs)  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 84, in __init__  
self.parse_orca_lines(lines, *args, **kwargs)  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 1755, in parse_orca_lines  
soc_oscillator_str.append(float(info[6]))  
^^^^^^^^^^^^^^  
ValueError: could not convert string to float: '('  
  
ValueError: could not convert string to float: '('  
  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 1755, in parse_orca_lines  
soc_oscillator_str.append(float(info[6]))  
^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> close

> open "H:/My
> Drive/Crespo/Rhodanines/5S/Water/6_S1_opt_freq/5S_water_S1_opt_freq_soc.out"

Summary of feedback from opening H:/My
Drive/Crespo/Rhodanines/5S/Water/6_S1_opt_freq/5S_water_S1_opt_freq_soc.out  
---  
error | unable to open 5S_water_S1_opt_freq_soc.out as a ORCA output file  
warnings | WARNING AaronTools.fileIO.FileReader.read_orca_out   
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR ***  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
  
================================================================================  
NAME = S1_opt_freq_soc.inp  
| 1> # Excite to get 8 singlet excited states and optimize S1  
| 2>  
| 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2  
CPCM(water)  
| 4>  
| 5> %maxcore 6000  
| 6>  
| 7> %base "5S_S1_opt_freq_1" #WATER!!!!  
| 8>  
| 9> %cpcm  
| 10> num_leb 302  
| 11> end  
| 12>  
| 13> %scf  
| 14> maxiter 300  
| 15> end  
| 16>  
| 17> %geom  
| 18> maxiter 300  
| 19> end  
| 20>  
| 21> %pal  
| 22> nprocs 16  
| 23> end  
| 24>  
| 25> %tddft  
| 26> NROOTS 8  
| 27>  
| 28> # Optimize S1  
| 29> IROOT 1  
| 30>  
| 31> # Which type of states for IROOT? singlet.  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR ***  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
  
================================================================================  
NAME = S1_opt_freq_soc.inp  
| 1> # Excite to get 8 singlet excited states and optimize S1  
| 2>  
| 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2  
CPCM(water)  
| 4>  
| 5> %maxcore 6000  
| 6>  
| 7> %base "5S_S1_opt_freq_1" #WATER!!!!  
| 8>  
| 9> %cpcm  
| 10> num_leb 302  
| 11> end  
| 12>  
| 13> %scf  
| 14> maxiter 300  
| 15> end  
| 16>  
| 17> %geom  
| 18> maxiter 300  
| 19> end  
| 20>  
| 21> %pal  
| 22> nprocs 16  
| 23> end  
| 24>  
| 25> %tddft  
| 26> NROOTS 8  
| 27>  
| 28> # Optimize S1  
| 29> IROOT 1  
| 30>  
| 31> # Which type of states for IROOT? singlet.  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR ***  
  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR ***  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
  
================================================================================  
NAME = S1_opt_freq_soc.inp  
| 1> # Excite to get 8 singlet excited states and optimize S1  
| 2>  
| 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2  
CPCM(water)  
| 4>  
| 5> %maxcore 6000  
| 6>  
| 7> %base "5S_S1_opt_freq_1" #WATER!!!!  
| 8>  
| 9> %cpcm  
| 10> num_leb 302  
| 11> end  
| 12>  
| 13> %scf  
| 14> maxiter 300  
| 15> end  
| 16>  
| 17> %geom  
| 18> maxiter 300  
| 19> end  
| 20>  
| 21> %pal  
| 22> nprocs 16  
| 23> end  
| 24>  
| 25> %tddft  
| 26> NROOTS 8  
| 27>  
| 28> # Optimize S1  
| 29> IROOT 1  
| 30>  
| 31> # Which type of states for IROOT? singlet.  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR ***  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR ***  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
  
================================================================================  
NAME = S1_opt_freq_soc.inp  
| 1> # Excite to get 8 singlet excited states and optimize S1  
| 2>  
| 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2  
CPCM(water)  
| 4>  
| 5> %maxcore 6000  
| 6>  
| 7> %base "5S_S1_opt_freq_1" #WATER!!!!  
| 8>  
| 9> %cpcm  
| 10> num_leb 302  
| 11> end  
| 12>  
| 13> %scf  
| 14> maxiter 300  
| 15> end  
| 16>  
| 17> %geom  
| 18> maxiter 300  
| 19> end  
| 20>  
| 21> %pal  
| 22> nprocs 16  
| 23> end  
| 24>  
| 25> %tddft  
| 26> NROOTS 8  
| 27>  
| 28> # Optimize S1  
| 29> IROOT 1  
| 30>  
| 31> # Which type of states for IROOT? singlet.  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR ***  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
  
================================================================================  
NAME = S1_opt_freq_soc.inp  
| 1> # Excite to get 8 singlet excited states and optimize S1  
| 2>  
| 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2  
CPCM(water)  
| 4>  
| 5> %maxcore 6000  
| 6>  
| 7> %base "5S_S1_opt_freq_1" #WATER!!!!  
| 8>  
| 9> %cpcm  
| 10> num_leb 302  
| 11> end  
| 12>  
| 13> %scf  
| 14> maxiter 300  
| 15> end  
| 16>  
| 17> %geom  
| 18> maxiter 300  
| 19> end  
| 20>  
| 21> %pal  
| 22> nprocs 16  
| 23> end  
| 24>  
| 25> %tddft  
| 26> NROOTS 8  
| 27>  
| 28> # Optimize S1  
| 29> IROOT 1  
| 30>  
| 31> # Which type of states for IROOT? singlet.  
  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR ***  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
  
================================================================================  
NAME = S1_opt_freq_soc.inp  
| 1> # Excite to get 8 singlet excited states and optimize S1  
| 2>  
| 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2  
CPCM(water)  
| 4>  
| 5> %maxcore 6000  
| 6>  
| 7> %base "5S_S1_opt_freq_1" #WATER!!!!  
| 8>  
| 9> %cpcm  
| 10> num_leb 302  
| 11> end  
| 12>  
| 13> %scf  
| 14> maxiter 300  
| 15> end  
| 16>  
| 17> %geom  
| 18> maxiter 300  
| 19> end  
| 20>  
| 21> %pal  
| 22> nprocs 16  
| 23> end  
| 24>  
| 25> %tddft  
| 26> NROOTS 8  
| 27>  
| 28> # Optimize S1  
| 29> IROOT 1  
| 30>  
| 31> # Which type of states for IROOT? singlet.  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
an error occured while reading the ORCA output file  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
last line read: *** ORCA-CIS/TD-DFT FINISHED WITHOUT ERROR ***  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
INPUT FILE  
  
================================================================================  
NAME = S1_opt_freq_soc.inp  
| 1> # Excite to get 8 singlet excited states and optimize S1  
| 2>  
| 3> ! pbe0 def2-SVPD RIJCOSX D3BJ def2/J autoaux opt LargePrint defgrid2  
CPCM(water)  
| 4>  
| 5> %maxcore 6000  
| 6>  
| 7> %base "5S_S1_opt_freq_1" #WATER!!!!  
| 8>  
| 9> %cpcm  
| 10> num_leb 302  
| 11> end  
| 12>  
| 13> %scf  
| 14> maxiter 300  
| 15> end  
| 16>  
| 17> %geom  
| 18> maxiter 300  
| 19> end  
| 20>  
| 21> %pal  
| 22> nprocs 16  
| 23> end  
| 24>  
| 25> %tddft  
| 26> NROOTS 8  
| 27>  
| 28> # Optimize S1  
| 29> IROOT 1  
| 30>  
| 31> # Which type of states for IROOT? singlet.  
  
WARNING AaronTools.fileIO.FileReader.read_orca_out  
the following data has been read: error, opt_steps, basis_set_by_ele,  
charge, multiplicity, n_basis, scf_energy, n_alpha, n_beta,  
alpha_coefficients, alpha_nrgs, alpha_occupancies, shell_to_atom, Mulliken  
Charges, Löwdin Charges, Mulliken gross atomic population, Total nuclear  
charge, Mulliken gross atomic charge, Mayer's total valence, Mayer's bonded  
valence, Mayer's free valence, uv_vis, CIS/TD root energy, dispersion  
correction energy, energy, forces, gradient, rotational_temperature,  
frequency, temperature, mass, ZPVE, enthalpy, molecular_point_group,  
rotational_symmetry_number, free_energy, soc x, soc y, soc z, soc (cm^-1),  
SOC GS stabilization energy  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py",
line 731, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py",
line 2117, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\\__init__.py", line 596, in open  
return open_aarontools(  
^^^^^^^^^^^^^^^^  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\io.py", line 46, in open_aarontools  
raise e  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\SEQCROW\io.py", line 33, in open_aarontools  
fr = FileReader(  
^^^^^^^^^^^  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\fileIO.py", line 1630, in __init__  
self.read_orca_out(f, get_all, just_geom, log=None)  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\fileIO.py", line 3189, in read_orca_out  
raise e  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\fileIO.py", line 3031, in read_orca_out  
self.other["uv_vis"] = ValenceExcitations(s, orca_version=orca_version,
style="orca")  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 1429, in __init__  
super().__init__(*args, **kwargs)  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 84, in __init__  
self.parse_orca_lines(lines, *args, **kwargs)  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 1755, in parse_orca_lines  
soc_oscillator_str.append(float(info[6]))  
^^^^^^^^^^^^^^  
ValueError: could not convert string to float: '('  
  
ValueError: could not convert string to float: '('  
  
File "C:\Users\Kushan\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\AaronTools\spectra.py", line 1755, in parse_orca_lines  
soc_oscillator_str.append(float(info[6]))  
^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

QWindowsWindow::setGeometry: Unable to set geometry 750x599+825+415 (frame:
768x646+816+377) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 748x591+826+422 (frame: 766x638+817+384)
margins: 9, 38, 9, 9 minimum size: 600x325 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=768, y=453)))  




OpenGL version: 3.3.0 - Build 32.0.101.5763
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: LENOVO
Model: 82X7
OS: Microsoft Windows 11 Home Single Language (Build 26100)
Memory: 8,267,882,496
MaxProcessMemory: 137,438,953,344
CPU: 6 13th Gen Intel(R) Core(TM) i3-1305U
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    Send2Trash: 1.8.3
    SEQCROW: 1.8.18
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1
File attachment: 5S_water_S1_opt_freq_soc.out

5S_water_S1_opt_freq_soc.out​

Attachments (1)

5S_water_S1_opt_freq_soc.out​ (78.6 MB ) - added by kst61@… 7 months ago.
Added by email2trac

Change History (5)

by kst61@…, 7 months ago

Attachment: 5S_water_S1_opt_freq_soc.out​ added

Added by email2trac

comment:1 by Eric Pettersen, 7 months ago

Component: Unassigned → Third Party
Owner: set to Tony Schaefer
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ORCA output: could not convert string to float

comment:2 by Eric Pettersen, 7 months ago

Reported by Kushan T

comment:3 by Tony Schaefer, 7 months ago 

Kushan,

Sorry for the delayed response. I wanted to make sure that the fix for this
wouldn't break the orca 6 parser, but I was having issues downloading orca
6. I'll upload the patch to the toolshed soon. It looks like the toolshed
site is down at the moment. In the meantime, you can download and install
seqcrow from github:
https://github.com/QChASM/SEQCROW/tree/master?tab=readme-ov-file#github

Thanks,

Tony

On Mon, Mar 31, 2025 at 11:24 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>

comment:4 by Eric Pettersen, 7 months ago 

The Toolshed is back again.

--Eric

>> #17232: ORCA output: could not convert string to float
>> ----------------------------------+---------------------------
>>           Reporter:  kst61@…      |      Owner:  Tony Schaefer
>>               Type:  defect       |     Status:  assigned
>>           Priority:  normal       |  Milestone:
>>          Component:  Third Party  |    Version:
>>         Resolution:               |   Keywords:
>>         Blocked By:               |   Blocking:
>> Notify when closed:               |   Platform:  all
>>            Project:  ChimeraX     |
>> ----------------------------------+---------------------------
>> Comment (by pett):
>> 
>>  Reported by Kushan T
>> -- 
>> Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17232#comment:2>
>> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
>> ChimeraX Issue Tracker
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