2021 AMBER tutorial 3 with PDBID 1S19
In this tutorial, we will be modeling ligand binding to our receptor using AMBER 16, a molecular dynamics simulation software package created in part by our very own Carlos Simmerling.
We will be saving all of our initial structures in a directory called 01.structure.
For the initial protein structure, we will be using the PDB we downloaded from the Protein Data Bank Website (see here). Load this PDB into chimera and delete the ligand and any nonstandard residues (ex. waters). Save this as a PDB file, 1s19_fresh.pdb, and transfer it to your 01.structure folder.
Generating Parameters for the Simulation
In order to utilize Amber for molecular dynamic, parameters for the bio molecules will be needed. Luckily, there have been years of parameter development so parameters for the protein do not have to worried about. However, the small ligand does not have parameters in the standard protein force field. Consequently, we will need to generate a fcmod file specific for the ligand.