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autoligand - Online in the Cloud

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This is the command autoligand 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



AutoLigand: - identification of a receptor's ligand binding site


It is suggested to start AutoLigand through the GUI that the autodocktools provide.
autoligand r FileBaseName -p #_of_pts The above is a simplification provided for the
Debian package. The regular command line invocation is through python
/usr/share/pyshared/AutoDockTools/AutoLigand.py -r FileBaseName -p #_of_pts


autoligand is a symbolic link to the Python script AutoLigand.py. That performs a an
automated investigation of the likelihood of a particular part of a protein to bind to

Description of command...

-r FileBaseName = just the name part from receptor map files (i.e., FileBaseName.C.map)

-p #_of_pts = number of fill points to use (int)

Note: can be omitted if -a option used.

Optional parameters:

[-a #] = number of heavy atom for ligand (#_of_pts will be set to 6x atoms) [-x #
-y # -z #] = optional x,y,z co-ords for starting fill (float)

when starting point is input, only one fill will be run

[-i # -j # -k #] = optional x,y,z co-ords for second point (float)

when second point is input, the fill will connect both points NOTE: the connection
path has not been optimized - use with discretion

[-f #] = number of fills to generate - default is 10 [-e] = use the extra atom
types NA, N, SA, and A

NOTE: these results can be problematic - use with discretion

[-m] = make a movie of output fill progress

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