2020 AMBER tutorial with PDBID 3VJK

In this tutorial, we will be modeling the dynamics of the ligand with the receptor using AMBER 16. Amber is a molecular dynamics simulation software package.

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.

First we will make a specific directory dedicated for the generation of the parameters for the ligand:

  mkdir 000.parameters

In this directory we will run the following command:

  antechamber -i ./../zzz.master/3VJK_ligand_hydrogens.mol2 -fi mol2 -o 3vjk_ligand_antechamber.mol2 -fo mol2 -at gaff2 -c bcc -rn LIG -nc 2

Build system with TLeap

https://ringo.ams.stonybrook.edu/images/5/54/3vjk_wet_10.jpg

https://ringo.ams.stonybrook.edu/images/c/c2/3vjk_solvated_wet8.jpg