> This gist contains some scripts for Amber. Maybe need some other tools installed, such as pdb2pqr and g09 and so on.

- [anteligand.sh](#file-anteligand-sh): Use antechamber to prepare a ligand for Amber
- [complex_tleap.sh](#file-complex_tleap-sh): Use tleap to prepare a ligand-protein complex input parameter file (Amber14)
- [checkPDBID_MDprep.sh](#file-checkpdbid_mdprep-sh): After running many preparation jobs for PDB ligand-protein complexes, you should check whether the preparation is done.
- [rename_water.py](#file-rename_water-py): rename water to HOH O,H1,H2 for PDB/PQR