2022 AMBER tutorial 1 with PDBID 6ME2

Introduction

AMBER is a program designed for computing biomolecular simulations. In this tutorial, AMBER will be used to simulate the dynamics between the ligand and receptor of the 6ME2 PDB file.

Directory Setup

For this tutorial, it is recommended to define the following directories to stay organized:

 mkdir 001_structure
 mkdir 002_parameters
 mkdir 003_leap
 mkdir 004_equil
 mkdir 005_production

6ME2 Structure Files

If the 6ME2 DOCK tutorials were followed before this AMBER tutorial, the user has some experience generating and prepping receptor and ligand filed from the original 6ME2 PDB file. However, it is recommended that the user NOT use the files generated in the 6ME2 DOCK tutorials and to instead start from scratch here, as this allows the chance to catch mistakes that may have been made but not recognized while following the initial DOCK tutorials.

To begin this tutorial, search the Protein Data Bank (PDB) website using the code 6ME2, or use the Fetch... button on the home screen of UCSF Chimera for this four-letter code. All the following structures should be saved to the following directory:

 cd 001_structure

Receptor File Generation

To generate a fresh copy of the receptor file, open the 6me2.pdb file containing the ligand-receptor complex. Go to

 Select -> Structure -> protein

which will select the receptor, and then go to

 Select -> Invert (all models)

to select everything other than the receptor in the file. Then, go to

 Actions -> Atoms/Bonds -> delete

which will isolate the receptor. Go to

 File -> Save Mol2... 

and save as 6me2_rec.mol2. Close Chimera.

Ligand File Generation

To generate the ligand file, open the 6me2.pdb file again, and go to

 Select -> Structure -> protein

then

 Actions -> Atoms/Bonds -> delete

to delete the receptor. Then, go to

 Select -> Residue -> HOH

 Select -> Residue -> OLA

 Select -> Residue -> PEG

to delete everything except for the JEV residue, which is the ligand of interest.

Note: there are problems with the file containing the ligand as-is. In order to proceed properly, it is necessary to make some changed to this file. While the file is still open, go to

 Tools > Structure Editing > Rotamers

and change the non-standard YCM residue to the most probable rotamers of CYS.

After this is completed, go to

 Tools > Structure editing > Add H

to add hydrogens to the ligand. Then, go to 

 Tools > Structure editing > Add Charge > (have Amber ff14SB and AM1-BCC selected) -> Ok

and then go to

 File -> Save Mol2... 

and save as 6me2_lig_dockprep.mol2. Close Chimera.

Generating Simulation Parameters

In order to generate parameters for this tutorial, switch to the following directory:

 cd 002_parameters

To generate the parameters, run the following command:

 antechamber -i ../001_structure/6me2_lig_wH.mol2 -fi mol2 -o 6me2_ligand_antechamber.mol2 -fo mol2 -at gaff2 -c bcc -rn LIG -nc 0

Note the -nc flag is set to 0 in the above line; this should correspond to the protonation state of the ligand. If a user is following this tutorial to simulate dynamics on a structure other than 6ME2, be sure to double check and change this value accordingly.

After the 6me2_ligand_antechamber.mol2 output file is generated, run the following command to run parmch2:

 parmchk2 -i 6me2_ligand_antechamber.mol2 -f mol2 -o 6me2_ligand.am1bcc.frcmod