In this tutorial, we will perform energy minimization and equilibration of a simple protein using NAMD [1] & VMD [2]. We are using insulin (PDB ID: 2wfu) for this tutorial.

Energy minimization is a process of searching for an energy landscape of the molecule to find a conformation of the molecule in which it is relaxed. The equilibration involves molecular dynamics whereby Newton’s Second Law is solved for each atom in the system to find its trajectory. Equilibration is judged by how well velocities, pressure, etc. are distributed in the system over a given amount of time.

Files required

Let’s start our minimization and equilibration using NAMD.

First, create a new directory namely, “namd”. We will save all our files inside this directory only.

1. Downloading PDB file of protein

Here, we are simulating insulin. Let’s download it from PDB (www.rcsb.org) and save it in the namd directory.

2. Preparing protein file

In this tutorial, we are simulating only chain A of the protein. Therefore, remove other chains from the PDB file and save it.

3. Generating a PSF file of protein

3.1. Creating protein file without Hydrogens

To generate a PSF file, we need the protein without hydrogens. Let’s create a new PDB file without hydrogens. To do this,

3.2. Generating PSF file

You can either generate a PSF file automatically using VMD or use the following commands to do the same. I would recommend the latter option because you will know what will happen at each step which will help you to catch errors easily. I personally use the manual method because the automatic builder gives errors at later stages including the file format error such as “FATAL ERROR: ABNORMAL EOF FOUND – buffer=*END*”. However, I will tell you the automatic method as well.

3.2.1. Using Automatic PSF builder

3.2.2. Using manual method

Again, open the Tk console in VMD. Type the following commands one by one.

% package require psfgen

% topology top_all27_prot_lipid.inp

% pdbalias residue HIS HSE

% pdbalias atom ILE CD1 CD

% segment U {pdb insp.pdb}

% coordpdb insp.pdb U

% guesscoord

% writepdb ins.pdb

% writepsf ins.psf

Remember, it will show you some warnings. You can avoid them. Ultimately, it will create two new files: ins.pdb and ins.psf.

Now, we have successfully generated a PSF file for the protein.

4. Solvating the protein

You can either minimize and equilibrate your protein in a water sphere (with non-periodic boundary conditions) in a surrounding vacuum or in a water box with periodic boundary conditions.

Visualize the protein in VMD now.

Get the x, y, and z coordinates and their maximum and minimum values of the entire protein-water system.

5. Minimization & equilibration

We will need a configuration file for this step where we will define our parameters for the simulation run. You can download the configuration file from here.

Open this file in an editor and edit accordingly.

Now finally, run the equilibration by typing the following command in a terminal (Ctrl+Alt+T):

$ /path/to/NAMD/namd3 box_sim.conf > ins_wb_eq.log &

It will take some time to finish and will output some files, out of which ins_wb_eq.dcd will be used for trajectory analysis.

The analysis will be explained in the upcoming article.


References

  1. Phillips, J. C., Hardy, D. J., Maia, J. D., Stone, J. E., Ribeiro, J. V., Bernardi, R. C., … & Tajkhorshid, E. (2020). Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of chemical physics153(4).
  2. Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: visual molecular dynamics. Journal of molecular graphics14(1), 33-38.