I packaged the OpenChemistry software needed to build Avogadro 2, from their respective latest master git commit, along with Avogadro 2 itself, using the openSUSE Build Service. Avogadro 2 launches fine, but there’s an issue with running obabel in it to optimize geometry. I started Avogadro 2 from the command-line so I could see the precise error messages and commands it is executing, this is what I saw when trying to optimize the geometry of a molecule:
OBProcess::executeObabel: Running "obabel" "-imol -omol --minimize --log --crit 1e-6 --ff --steps 10000 --rvdw 10 --rele 10 --freq 10" MDL: "Open Babel 2.4.90 -- May 28 2018 -- 20:57\nUsage:\nobabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]\nTry -H option for more information.\n"
seems like the command is not found. Open Babel must be working somewhat given that I managed to open a SDF file, which I think requires the Open Babel backend to work. I tried a few example Open Babel 3 commands, however, and they all returned errors. Like when I ran the example command:
obabel -:"O=C(O)c1ccccc1OC(=O)C aspirin" -:"Oc1ccccc1C(=O)O salicylic acid" -ofpt
(per the docs for 2.3.1, not sure if Open Babel 2 and 3 use the same syntax, however)
I received the output:
obabel: cannot write output format! Open Babel 2.4.90 -- May 28 2018 -- 20:57 Usage: obabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options] Try -H option for more information.
If you want to look at the files I used to build Open Babel 3, here they are. If you want to see the build log click the “Succeeded text” next to the “openSUSE Tumbleweed” build target on the right side bar. Here’s a screenshot showing exactly what I mean for the Avogadro 2 libraries package:
. Avogadro 2 (i.e. avogadroapp) is here. The libraries (avogadrolibs) are here. MoleQueue is packaged here. spglib is here. I tried running an strace on the aspirin obabel command above, here is the output:
Here is strace output for opening a SDF file with Avogadro 2 and trying to optimize the geometry:
I really want this Avogadro 2 build to work to its fullest potential so please, if there’s something you need to know in order to help fix this ask.
I’ve also tried editing avogadro2-libs, removing all patches and adjusting the spec file so the build occurs properly (as it changes the contents of the packages), and I get the same obabel issues.
Thanks for your time,