vina1

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