Progesteron Receptor

Objective

To explore the protein-ligand conformational space around the binding site. Useful to refine docking

Preparation

To start the simulation, we need the complex.pdb an the input.yaml

Receptor

Process the protein complex (PDB id: XXXX) with Protein Preparation Wizard (Schrodinger Program Suite) at pH 7.4 ± 0.5 to assign the protonation state to all ionizable residue as well as optimize the H-bond network. (Already done)

Procedure: Induced fit

Main characteristics of the simulation

• Induced fit simulation

• Inversely proportional strategy

• Computational time: 4h

• Cpus: 64

Control File Specifics

system: 'PR_1A28_xray_-_minimized.pdb'
chain: 'Z'
resname: 'STR'
seed: 12345
induced_fit_fast: true
cpus: 64

Launch Command

python -m pele_platform.main input.yaml