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).
-
When visualising the trajectory
- Draw atomic distances
- Increase visualization windows size
- Showing water and ions
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When plotting
- Add vertical line option
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For analysis
- Probability of being at a catalytic relevant distance (i.e., residence time)
- Classify structures by local minima.
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For prepare_ligand.py script
- Add water solvent to Jaguar optimization