Launch your first jobΒΆ

0) Prepare the system with maestro (Protein Preparation Wizard, hydrogen optimization and posterior minimization) and output a complex.pdb

1) Copy the text below into a file called input.yaml and change the path to your input pdb file, the residue name of the ligand to be perturb and its chain.

system: "complex.pdb"
residue: "LIG"
chain: "L"

  1. Choose one of the modes below by copying its line to the input.yaml:

induced_fit: true
out_in: true
in_out: true
global: true

  1. Test your simulation (1min):

First add the flag test:true into and launch the next command:

python -m pele_platform.main input.yaml

  1. Run prodution

If everything works change the flag test: true by cpus: X being X the number of cpus to use for the job. From 40-60 for induced fit simulation and exit paths, from 100-200 for local explorations and 250 for global. Finally run the python command again:

python -m pele_platform.main input.yaml