-gmxscreen

MIPkit -gmxscreen ...

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This command takes a combination of -screen and -interact arguments. The most relevant ones are listed here.

-screen arguments

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

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

-fms : string, default None
Which functional monomers to screen. If left blank, all FMs will be screened.

-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.

-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.

-interact arguments

-fs : str, default None
Timestep in femtoseconds. Options are 05 (0.5), 1 (1.0), 2 (2.0).

-gpu_id : int, default None
A direct wrap to the command in GROMACS. Sets the GPU ID number in machines with multiple GPUs.

-ns : int, default None
Nanosecond duration for interaction to occur. Options are 50, 100, 300, and 500.

-solvent : string, named. default spc
The solvent in the system. Defaults to water, but DMSO is also currently supported. Additional solvents will be added as needed.