10.2 Building Systems - CHARMM-GUI
Some people find it easier to set up a system for simulation in Amber using the CHARMM-GUI interface. These tutorials were written by Wonpil Im at Lehigh University. He also has You Tube videos on these tutorials.
10.2.1 Available AMBER FFs in CHARMM-GUI
List of AMBER forcefields available in CHARMM-GUI. Before you begin, make sure the Amber force field you require to simulate your system is included in CHARMM-GUI.
10.2.2 Preparation of protein/N-glycan/ligand/membrane complex (5O8F)
This is a tutorial on how to use CHARMM-GUI to set up a system to run MD in AMBER. The example system if fairly complicated in that there are multiple biomolecules (protein, carbohydrate, lipids and an organic ligand).
This video guides the user through setting up the pdb "5O8F" using AMBER force fields and inputs with CHARMM-GUI.
10.2.4 Changing Protonation State with PDB2PQR and reading AMBER FF residue
PDB files frequently require changes in protonation state. Manually ensuring that each residue has the correct hydrogen count is tedious and error prone. In this demo, the Im Lab shows how to (1) prepare a PDB file (6IYC) with a realistic protonation state at pH 7 using the PDB2PQR server, (2) read a PDB file containing Amber FF residue names, and (3) generate a hexagonal membrane system for simulation with the AMBER force fields.
Note that the PDB2PQR server is used in this example and there are other servers that do similar jobs.