avogadrolibs: Optimize geometry with Force Field | Error interpreting Open Babel output

Versions:

Avogadro2: 1.97.0.r837.8ec3eb4-1
Avogadrolibs: 1.97.0.r2930.d610df7a-1
Openbabel: openbabel 3.1.1-4

Desktop version: distro: Manjaro Linux base: Arch Linux kernel: 5.10.136-1 arch: x86_64 desktop: GNOME v: 42.4

Description of the bug: I get this error when trying to optimize geometry with a Force Field: “Error interpreting Open Babel output.”

error_babel

To Reproduce: Steps to reproduce the behaviour:

launch avogadro2
Click on “Draw tool”
In the left panel menu, “Element”, select “Carbon (6)”, and draw a CH4 molecule.
Click on “Extensions” > “Open Babel” > “Configure Force Field” Select “UFF” Force field, “Conjugate Gradient”, “Simple” technique, Select “Energy convergence to 10 ^-6 units” and “Step limit to 100000 steps”
Click “Ok”.
Click on “Extensions” > “Open Babel” > “Optimize Geometry”
The error appears (above screenshot).

Terminal output

1. When launching avogadro2:

$ avogadro2 
Using locale:  "en_DK"
Extension plugins dynamically found… 40
OBProcess::executeObabel: Running "obabel" "-L formats read"
OBProcess::executeObabel: Running "obabel" "-L formats write"
OBProcess::executeObabel: Running "obabel" "-L forcefields"
OBProcess::executeObabel: Running "obabel" "-L charges"
OBProcess::executeObabel: Running "obabel" "-V"
"obabel"  found:  "obabel: Open Babel 3.1.0 -- Jul  7 2022 -- 17:58:53"
Checking for  "commands"  scripts in "/home/david/.local/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/home/david/.local/share/flatpak/exports/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/var/lib/flatpak/exports/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/usr/local/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/usr/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/usr/bin/../lib/avogadro2/scripts/commands"
Checking for  "inputGenerators"  scripts in "/home/david/.local/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/home/david/.local/share/flatpak/exports/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/var/lib/flatpak/exports/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/usr/local/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/usr/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/usr/bin/../lib/avogadro2/scripts/inputGenerators"
Checking for  "formatScripts"  scripts in "/home/david/.local/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/home/david/.local/share/flatpak/exports/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/var/lib/flatpak/exports/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/usr/local/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/usr/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/usr/bin/../lib/avogadro2/scripts/formatScripts"
Checking for  "charges"  scripts in "/home/david/.local/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/home/david/.local/share/flatpak/exports/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/var/lib/flatpak/exports/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/usr/local/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/usr/share/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/charges"
Checking for  "charges"  scripts in "/usr/bin/../lib/avogadro2/scripts/charges"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/usr/lib/avogadro2/scripts/charges/antechamber.py" ; "Error running script '/usr/bin/python /usr/lib/avogadro2/scripts/charges/antechamber.py --display-name --lang en_DK': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/usr/lib/avogadro2/scripts/charges/antechamber.py\", line 151, in <module>\n    raise RuntimeError(\"antechamber is unavailable\")\nRuntimeError: antechamber is unavailable\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/usr/lib/avogadro2/scripts/charges/xtb.py" ; "Error running script '/usr/bin/python /usr/lib/avogadro2/scripts/charges/xtb.py --display-name --lang en_DK': Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n  File \"/usr/lib/avogadro2/scripts/charges/xtb.py\", line 100, in <module>\n    raise RuntimeError(\"xtb is unavailable\")\nRuntimeError: xtb is unavailable\n"
Open Babel formats ready:  145

b) When performing steps 1-7 above:

OBProcess::executeObabel: Running "obabel" "-icml -ocml --minimize --noh --log --crit 1e-06 --ff UFF --steps 100000 --rvdw 10 --rele 10 --freq 10"

c) When clicking “OK” in the above screenshot:

Open Babel: ""
Process encountered an error, and did not execute correctly.
	Exit code: 6
	Exit status: QProcess::CrashExit
	Exit output: ""

The error message appears again. If I click “OK” again, terminal window prints:

Open Babel: ""

About this issue

Original URL
State: closed
Created 2 years ago
Comments: 15 (9 by maintainers)

Most upvoted comments

@ghutchis Many thanks for your reply. Please find detailed answers to your questions below.

It looks like you built this from source? Or is the Open Babel from your distro package?

So, avogadrolibs and avogadro2 were built using Arch Linux AUR repositories, respectively:

avogadrolibs-git here: https://aur.archlinux.org/packages?O=0&K=avogadrolibs
avogadro2-git here: https://aur.archlinux.org/packages?O=0&K=avogadro2

And the way I built those was through the standalone Arch Linux AUR package manager - there are several available, and a very good one is yay, i.e. simply:

yay -S avogadrolibs-git yay -S avogadro2-git

commands that essentially grab the packages from the links above, and then they do the building automatically.

Regarding Open Babel, I used the openbabel 3.1.1-4 available in Arch Linux, in the section for “Packages”: https://archlinux.org/packages/extra/x86_64/openbabel/ And I installed it following the same command as before: yay -S openbabel

If you Export a file to .cif or .mopin (which force Open Babel use) does that work?

So,

Launch avogadro2
Click on “Draw tool”
In the left panel menu, “Element”, select “Carbon (6)”, and draw a CH4 molecule.
In the top panel menu, I click on “Molecule” and save as ch4.cif

The terminal window prints:

 writing to  cml
OBProcess::executeObabel: Running "obabel" "-icml -ocif"

And the file is generated successfully.

Similarly, if I save as ch4.mopin, the terminal window prints:

 writing to  cml
OBProcess::executeObabel: Running "obabel" "-icml -omopin"

And the file is generated successfully.

If you draw a molecule and then go to View => Color => By Partial Charge … what do you see?

So,

Launch avogadro2
Click on “Draw tool”
In the left panel menu, “Element”, select “Carbon (6)”, and draw a CH4 molecule.
“View” > “Color Atoms” > “By Partial Charge” prompts this window:

window

If I click “OK” I get this: this

And the terminal window prints:

OBProcess::executeObabel: Running "obabel" "-icml -onul --partialcharge eem --print"

DavidCdeB on Aug 17, 2022