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-dock

MIPkit -dock ...

-config : string, default None
The recomended docking approach. Specifies all or some inputs in the config rather than via command line.

-dockmethod : string, default gnina
Specifies whether to use Vina or gnina for docking.

-fms : string int ... , default None
Takes the place of -config in specifying the functional monomer names and count to be docked. For example, -dock -fms NIPAM 15 AAC 10 BIS 2 will dock 15 NIPAM, 10 AAC, and 2 BIS.

-gmxprotein : string, default None
Gromacs processed PDB file used as a docking target in Vina and GROMACS.

-ncpu : int, default #
Number of physical CPU cores to use in both Vina and GROMACS. -1 will use all detected CPUs. Default is a quarter of the physical CPUs detected, rounded down to the nearest 2^n (GROMACS and LAMMPS do weird things with odd CPU counts).

-protein : string, default None
PDB file used as a docking target in Vina and GROMACS. For PDB proteins, -protein should be used instead of -template. If already processed with pdb2gmx, use -gmxprotein instead.

-scale : int, default 1
This command scales the FM recipe by multiplying the number of functional monomers by the scaled amount. This allows for increasing systems in order to determine saturation.

-serial : none, default False
If -serial is flagged, the functional monomers will be docked in the order in which they are specified. For example, 15 NIPAM, 10 AAC, and 2 BIS will dock all 15 NIPAM, then 10 AAC, then the 2 BIS. This can be used to determine whether docking functional monomers before crosslinkers is important to performance or not.

-shuffle : none, default True
Shuffles the input FM. So, for 5 NIPAM, 1 AAC, and 2 BIS, we might see a docked order of [ NIPAM, BIS, BIS, AAC, NIPAM, NIPAM, NIPAM, NIPAM ].

-shuffle_seed : string, default xF00D
Controls the shuffle order. This is necessary for validation.

-template : string, default None
PDB file used as a docking target in Vina and GROMACS. -template should be used for non-protein targets, as it avoids the use of pdb2gmx in GROMACS which will throw an error.