Building Simulation Boxes for ABFE Calculations (Tyk2)

Zeke A. Piskulich¹, Patricio Barletta¹, Ryan Snyder¹, and Darrin M. York¹

¹Laboratory for Biomolecular Simulation Research, Institute

for Quantitative Biomedicine and Department of Chemistry and Chemical

Biology, Rutgers University, Piscataway, NJ 08854, USA

Learning objectives

Learn how to build simulation boxes for absolute binding free energy calculations (ABFE) using AmberTools
Understand the options for solvating simulation boxes and adding ions
Learn how to make consistent solvent boxes for both the bound and unbound states of the ligand.

Relevant literature

Coming Soon!

Tutorial

In this Tutorial, you will learn how to set up and run absolute binding free energy calculations using Amberflow, a workflow engine developed in the York Lab for automating Alchemical Free Energy Calculations with Amber.

Building Simulation Boxes for ABFE Calculations 

To get started, you will need to download the tutorial files. The files include pdbs for the protein, and pdbs with docked coordinates for the ligand. The files in this download also include pre-generated forcefield parameters for each of the four ligands, which you will use in this tutorial.

Download the tutorial files

Once you have downloaded the files, extract them into a directory where you will be working on this tutorial.

tar -xvzf build_files.tar.gz
cd build_files

Building the Ligand in the Aqueous Phase 

In this section, you will build the ligand in a solvent box. You will be using tleap to build the system.

For this tutorial, we will be starting with the ligand ejm_31 and doing both builds for the bound and unbound states with this ligand. We will then be using the same procudure for the other three ligands. For each code block below, we have provided tabs for the other ligands so that you can easily switch between them.

Warning

In this tutorial, we will not be making a significant effort to enforce best practices for preparing the solvent box. In a production settign, you likely will desire to enforce that the solvent box has the same number of water molecules for all ligands, and depending on the identity of the ligand you may want to use a different box size or shape.

To build the ligand in a solvent box, you will need to create a tleap input file.

ejm_31

source leaprc.protein.ff19SB
source leaprc.phosaa19SB
loadamberparams frcmod.ff19SB
source leaprc.gaff2
source leaprc.water.tip4pew
loadamberparams frcmod.tip4pew
loadamberparams frcmod.ionsjc_tip4pew

loadoff ../binder_ejm_31.lib
loadamberparams ../binder_ejm_31.frcmod

mol = loadpdb ../binder_ejm_31.pdb

setbox mol centers
addions2 mol Na+ 0
addions2 mol Cl- 0

solvateoct mol TIP4PBOX 16.0

saveamberparm mol prebox_binder_ejm_31.parm7 prebox_binder_ejm_31.rst7
quit

ejm_42

source leaprc.protein.ff19SB
source leaprc.phosaa19SB
loadamberparams frcmod.ff19SB
source leaprc.gaff2
source leaprc.water.tip4pew
loadamberparams frcmod.tip4pew
loadamberparams frcmod.ionsjc_tip4pew

loadoff ../binder_ejm_42.lib
loadamberparams ../binder_ejm_42.frcmod

mol = loadpdb ../binder_ejm_42.pdb

setbox mol centers
addions2 mol Na+ 0
addions2 mol Cl- 0

solvateoct mol TIP4PBOX 16.0

saveamberparm mol prebox_binder_ejm_42.parm7 prebox_binder_ejm_42.rst7
quit

jmc_27

source leaprc.protein.ff19SB
source leaprc.phosaa19SB
loadamberparams frcmod.ff19SB
source leaprc.gaff2
source leaprc.water.tip4pew.. tab-set::
loadamberparams frcmod.tip4pew
loadamberparams frcmod.ionsjc_tip4pew

loadoff ../binder_jmc_27.lib
loadamberparams ../binder_jmc_27.frcmod

mol = loadpdb ../binder_jmc_27.pdb

setbox mol centers
addions2 mol Na+ 0
addions2 mol Cl- 0

solvateoct mol TIP4PBOX 16.0

saveamberparm mol prebox_binder_jmc_27.parm7 prebox_binder_jmc_27.rst7
quit

jmc_28

source leaprc.protein.ff19SB
source leaprc.phosaa19SB
loadamberparams frcmod.ff19SB
source leaprc.gaff2
source leaprc.water.tip4pew
loadamberparams frcmod.tip4pew
loadamberparams frcmod.ionsjc_tip4pew

loadoff ../binder_jmc_28.lib
loadamberparams ../binder_jmc_28.frcmod

mol = loadpdb ../binder_jmc_28.pdb

setbox mol centers
addions2 mol Na+ 0
addions2 mol Cl- 0

solvateoct mol TIP4PBOX 16.0

saveamberparm mol prebox_binder_jmc_28.parm7 prebox_binder_jmc_28.rst7
quit

To run any of these scripts, save the desired script (e.g., tleap_ejm_31.in) and then run the following command:

tleap -f tleap_ejm_31.in

Optional: Applying Hydrogen Mass Reparationing (HMR)

Often, in order to speed up simulations, we will apply hydrogen mass repartitioning (HMR) to the system. This allows us to use a larger timestep (4 fs vs 2 fs) for production simulations.

To do this, we will be using the ParmEd package that comes with AmberTools. The following command will apply HMR to a given topology and coordinate file, and output new files with HMR applied.

We will need to make a parmed input file for each of the systems. Here is an example for ejm_31 in complex:

ejm_31

parm target_ejm_31.parm7
hmassrepartition
outparm target_ejm_31_hmr.parm7

ejm_42

parm target_ejm_42.parm7
hmassrepartition
outparm target_ejm_42_hmr.parm7

jmc_27

parm target_jmc_27.parm7
hmassrepartition
outparm target_jmc_27_hmr.parm7

jmc_28

parm target_jmc_28.parm7
hmassrepartition
outparm target_jmc_28_hmr.parm7

The same can be done for the binder:

ejm_31

parm binder_ejm_31.parm7
hmassrepartition
outparm binder_ejm_31_hmr.parm7

ejm_42

parm binder_ejm_42.parm7
hmassrepartition
outparm binder_ejm_42_hmr.parm7

jmc_27

parm binder_jmc_27.parm7
hmassrepartition
outparm binder_jmc_27_hmr.parm7

jmc_28

parm binder_jmc_28.parm7
hmassrepartition
outparm binder_jmc_28_hmr.parm7

These files can be run using the following command:

parmed -i parmed_ejm_31.in

For simplicity, a script to do this for all four ligands is provided below:

for ligand in ejm_31 ejm_42 jmc_27 jmc_28; do
    echo "parm target_${ligand}.parm7" > parmed_${ligand}_target.in
    echo "hmassrepartition" >> parmed_${ligand}_target.in
    echo "outparm target_${ligand}_hmr.parm7" >> parmed_${ligand}_target.in

    echo "parm binder_${ligand}.parm7" > parmed_${ligand}_binder.in
    echo "hmassrepartition" >> parmed_${ligand}_binder.in
    echo "outparm binder_${ligand}_hmr.parm7" >> parmed_${ligand}_binder.in

    parmed -i parmed_${ligand}_target.in
    parmed -i parmed_${ligand}_binder.in
done

Building Simulation Boxes for ABFE Calculations (Tyk2)

Learning objectives

Relevant literature

Tutorial

Building Simulation Boxes for ABFE Calculations 

Building the Ligand in the Aqueous Phase 

Calculating the Number of Ions to Add 

Building the Bound Protein-Ligand Complex 

Optional: Applying Hydrogen Mass Reparationing (HMR)

Building Simulation Boxes for ABFE Calculations (Tyk2)

Learning objectives

Relevant literature

Tutorial

Building Simulation Boxes for ABFE Calculations

Building the Ligand in the Aqueous Phase

Calculating the Number of Ions to Add

Building the Bound Protein-Ligand Complex

Optional: Applying Hydrogen Mass Reparationing (HMR)

Building Simulation Boxes for ABFE Calculations 

Building the Ligand in the Aqueous Phase 

Calculating the Number of Ions to Add 

Building the Bound Protein-Ligand Complex 