protein ligand docking

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protein ligand docking

Matthias Bernt
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-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. 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



--

-------------------------------------------
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,
[hidden email], www.ufz.de

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Prof. Dr. Heike Graßmann
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