Difference between revisions of "2021 AMBER tutorial 3 with PDBID 1S19"
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== Protein == | == Protein == | ||
| − | For the initial protein structure, we will be using the PDB we downloaded from the Protein Data Bank Website see [https://www.rcsb.org/structure/1s19 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. | + | For the initial protein structure, we will be using the PDB we downloaded from the Protein Data Bank Website (see [https://www.rcsb.org/structure/1s19 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. |
== Ligand == | == Ligand == | ||
Revision as of 18:45, 1 April 2021
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.
Contents
Initial Structures
We will be saving all of our initial structures in a directory called 01.structure.
Protein
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.
Ligand
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.
