- anteligand.sh: Use antechamber to prepare a ligand for Amber
- complex_tleap.sh: Use tleap to prepare a ligand-protein complex input parameter file (Amber14)
- checkPDBID_MDprep.sh: After running many preparation jobs for PDB ligand-protein complexes, you should check whether the preparation is done.
- rename_water.py: rename water to HOH O,H1,H2 for PDB/PQR
Maybe need some other tools installed, such as pdb2pqr and g09 and so on.