09-21-2011
Well, it means what it says: it can't find vina.
If it's in the current directory, you have to run it as ./vina
Otherwise, try whereis vina, that might tell you where it is. If it's in an odd location you'd run it as /path/to/vina
You don't want $vina, that's how you'd use a variable named vina. That must be blank, causing the line to become --config ... and of course it can't find any file to run named '--config' either.
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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)