This is the command vina 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
PROGRAM:
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
Use vina online using onworks.net services
