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autodock4 - Online in the Cloud

Run autodock4 in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command autodock4 that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



autodock - docking of chemical ligands to protein receptors


autodock4 [options]


AutoDock perfoms the automated docking of chemical compounds to proteins, i.e. it predicts
how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D

The AutoDockSuite consists of two main programs of which AutoDock performs the docking of
the ligand to a set of grids describing the target protein and AutoGrid pre-calculates
these grids.


-p parameter_filename

-l log_filename

-o Use old PDBQ format, charge q in columns 55-61

-k Keep original residue numbers

-i Ignore header-checking

-t Parse the PDBQ file to check torsions, then stop.

-c < command_file Command mode, by file

-c | control_program Command mode, by control_program


On Debian, the directory /usr/share/doc/autodock offers examples to run. Change to that
directory and unpack (as root) the gzipped map files, then execute AutoDock as shown
gunzip *.map.gz
autodock4 -p 1pgp.dpf -l /tmp/1pgp.dlg

The interpretation of results is aided by the AutoDockTools suite. Please also inspect the
tutorials offered online.

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