Simulation

Start your own simulation:

  1. Complex Preparation

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

Make sure the ligand has:

  • Unique chain

  • No atomnames with spaces or single letter

  • Any residuename except UNK

  1. Prepare the input file input.yml

For more on the input files and the different types of simulation, please, refere to here

  1. Run the simulation

python -m pele_platform.main input.yml