Dear list,
I have recently evaluated the software for protein docking that is available in the toolshed. I could need some help / suggestions.
1. autodock_vina
The receptor of my example contains Au atoms which are not understood by autodock_vina. For autodock there is the possibility to add configuration for atoms:
http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-a...
Does somebody know if this is also possible for autodock_vina in galaxy?
In my pdb file there are CONECT lines which cause autodock_vina to abort. If I remove them the program runs (when the Au atoms are also removed). So this is the smaller problem (Maybe this can be solved by extending openbabel).
2. rdock
Fails with a memory access failure
/gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda/envs/__rDock@2013.1/bin/rbcavity: Zeile 7: 104454 Speicherzugriffsfehler (Speicherabzug geschrieben) "$RBT_ROOT/bin/$PROGNAME" "$@"
3. caddsuite_workflows + caddsuite_linux_x86_64
The installation of the workflows works, but I do not see them in galaxy?
The installation of the other package fails with:
No information is available for the requested repository revision. One or more of the following parameter values is likely invalid: tool_shed_url: https://toolshed.g2.bx.psu.edu/ name: caddsuite_linux_x86_64 owner: marcel changeset_revision: 026f5a483650
err_code: 400008
4. BALL
I just tested one tool of the suite: ProteinProtonator. This fails with command not found.
Fatal error: Exit code 127 () /gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/000/165/tool_script.sh: Zeile 9: ProteinProtonator: Kommando nicht gefunden.
Are there any suggestion on how to solve these problems or other options for docking with galaxy.
Cheers, Matthias
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