05-02-2005
the reason why it was not working is due to the fact this is a new option for Aix 5.3. I was trying to get this to work on Aix 5.2. The problem was I was doing a search on IBM' pSeries and Aix Information center and I could not tell which version this applied to.
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AUTODOCK(1) General Commands Manual AUTODOCK(1)
NAME
vina - docking small molecules against proteins
DESCRIPTION
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
SEE ALSO
AutoDock Vina home page on http://vina.scripps.edu.
AutoDock Vina 1.1.1 (Apr 20, 2010) November 2010 AUTODOCK(1)