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.

We will need to have some structures for running the simulation. This can be all stored in a directory called zzz.master. In this directory we will have the following files:

3vjkFH.pdb  3VJK_hydrogen_protein.mol2  3VJK_ligand_hydrogens.mol2

Please note that 3VJK_hydrogen_protein.mol2 had to be converted to a pdb using tleap because there were incapability issues that arose in a later step. To convert you do the following:

  tleap
  rec= loadmol2 3VJK_hydrogen_protein.mol2 
  save rec 3vjkFH.pdb  
  quit 

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