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 Post subject: Autodock Vina tutorial
PostPosted: Sat Nov 08, 2014 10:48 am 
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Joined: Mon Nov 03, 2014 8:16 pm
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I have problem with configuration file from Autodock Vina tutorial. I get the next error:
MacBook-Air-MacBookAir:bin MacBookAir$ ./vina --config config.txt --log log.txt
Configuration file parse error: unknown option all

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

MacBook-Air-MacBookAir:bin MacBookAir$

Here is my config.txt file:
receptor = 1SA1-C-D.pdbqt
ligand = 12f.pdbqt

all = all.pdbqt

center_x = 45.401
center_y = 53.718
center_z = -5.923

size_x = 126
size_y = 126
size_z = 126

exhaustiveness = 8


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