Prepare your own binding simulation

This simulation aims to find the binding path of a small molecule to a given receptor.

Input (further explained below):

• protein-ligand pdb

Output (further explained below):

• ranked binding modes of the chosen small molecule with the desired protein

Computational Time: 6h

1. Complex Preparation

Prepare the system with maestro (Protein Preparation Wizard) and output a complex.pdb. The complex.pdb must contain the protein-ligand in the desired initial conformation. If the binding site is known, the ligand must be set as close as possible to the protein surface on that side of the protein.

2. Input Preparation

Prepare the input file input.yml:

system: 'docking2grid6n4b_thc.pdb' #Protein ligand pdb
chain: 'L' #Ligand chain name
resname: 'THC' # Ligand residue name
seed: 12345
#Distance to track along the simulation
atom_dist:
- "A:2:CA" #First atom to make the distance to
- "B:3:CG" #Second atom to make the distance to
cpus: 200
out_in: true

For more optional flags please refer to optative falgs

3. Run simulation

To run the system launch the simulation with the next command:

python -m pele_platform.main input.yml

4. Output

Best ranked clusters:

working_folder/results/clusters

Best ranked poses:

working_folder/results/BestStructs/