PELE_scripts

Scripts for PELE:

-ligand_setup.py

Calculates multiconfigurational RESP charges:

Usage:

$SCHRODINGER/run python3 ligand_setup.py ligand_pdb_file three_letter_residue_name 

For other options run only:

$SCHRODINGER/run python3 ligand_setup.py

The final output file is found in folder 03_resp_charges (the only .mae file there).

PELE analysis

Pending implementation

• When visualising the trajectory

  • Draw atomic distances
  • Increase visualization windows size
  • Showing water and ions

• When plotting

  • Add vertical line option

• For analysis

  • Probability of being at a catalytic relevant distance (i.e., residence time)
  • Classify structures by local minima.

• For prepare_ligand.py script

  • Add water solvent to Jaguar optimization