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AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
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PostPosted: Wed Feb 12, 2014 9:45 am 
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Millimolar User
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Joined: Wed Feb 12, 2014 9:34 am
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Hi,
I am new to Linux, installed Ubuntu 13.10 on my Desktop; downloaded autodock from Ubuntu Software Center, and installed Autodock, but dont know why it doesnt open. when I click Alt+f2, the icon will open, but doesnt get activated upon clicking. I tried to download autodock and copy into usr/local/bin but it doesnt copy as well.
Could you please suggest me how best Install or verify as whether its installed properly and work on Autodock..
Sincerely,
Dr. Raghavendra
Professor,
Gokaraju Rangaraju College of Pharmacy,
Hyderabad, AP, India
Email: nmraghav7@gmail.com


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PostPosted: Thu Feb 20, 2014 10:42 pm 
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Joined: Sun Jun 21, 2009 11:37 pm
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To verify that autodock vina or autodock4 is installed correctly, invoke the program without all of its required arguments.
If the program is installed correctly but required input is missing, a usage message similar to the following will be printed:

% vina
Missing receptor.

Correct usage:

Input:
--receptor arg rigid part of the receptor (PDBQT)
--flex arg flexible side chains, if any (PDBQT)
--ligand arg ligand (PDBQT)

Search space (required):
--center_x arg X coordinate of the center
--center_y arg Y coordinate of the center
--center_z arg Z coordinate of the center
--size_x arg size in the X dimension (Angstroms)
--size_y arg size in the Y dimension (Angstroms)
--size_z arg size in the Z dimension (Angstroms)

Output (optional):
--out arg output models (PDBQT), the default is chosen based on
the ligand file name
--log arg optionally, write log file

Misc (optional):
--cpu arg the number of CPUs to use (the default is to try to
detect the number of CPUs or, failing that, use 1)
--seed arg explicit random seed
--exhaustiveness arg (=8) exhaustiveness of the global search (roughly
proportional to time): 1+
--num_modes arg (=9) maximum number of binding modes to generate
--energy_range arg (=3) maximum energy difference between the best binding
mode and the worst one displayed (kcal/mol)

Configuration file (optional):
--config arg the above options can be put here

Information (optional):
--help display usage summary
--help_advanced display usage summary with advanced options
--version display program version


% autodock4
usage: AutoDock -p parameter_filename
-l log_filename
-k (Keep original residue numbers)
-i (Ignore header-checking)
-t (Parse the PDBQT file to check torsions, then stop.)
-d (Increment debug level)
-C (Print copyright notice)
--version (Print autodock version)
--help (Display this message)


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