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 savepdb rec 3vjkFH.pdb quit
First we will make a specific directory dedicated for the generation of the parameters for the ligand:
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
notice that will be using gaff2. This stands for general amber force field 2. This will allow us to parameterize ligands for simulations. Additionally, the ligand has a charge of +2 and that was noted with the -nc flag. Once this command has run, it is beneficial to check to find if any parameters are missing:
parmchk2 -i 3vjk_ligand_antechamber.mol2 -f mol2 -o 3vjk_ligand.am1bcc.frcmod
The output shows that the parameters that were generated were sufficient to continue.