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_vinaThe 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-autodock 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. BALLI 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 -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.be...@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus
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