How to generate PSF file for MD simulation using NAMD & VMD?

Protein structure file (PSF) contains topology information and is required for molecular dynamics (MD) simulation in NAMD [1] and VMD [2]. In this tutorial, we will generate a PSF file of a simple protein using NAMD and VMD.

Contents

Generating a PSF file of protein 1. Loading the Protein file in VMD 2. Creating the protein file without Hydrogens 3.1. Generating PSF file 3.1.1. Using Automatic PSF builder 3.1.2. Using manual method References Further Reading

There are two methods of generating a PSF file in VMD:

Manual method
Automatic PSF builder

We will go through both these methods in detail. We are using a simple insulin protein (PDB ID: 2wfu) for this tutorial. Before proceeding further, we need to create a protein file without hydrogens. This protein file will then be used to generate its PSF file.

Generating a PSF file of protein

1. Loading the Protein file in VMD

Open VMD by typing $ vmd in a terminal.
In the main VMD window, go to File –> New Molecule. Molecule File Browser window will open.
Browse for the 2wfu.pdb –> Click OK –> Click Load.

2. Creating the 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,

In the main VMD window, go to Extensions –> Tk Console. A new console window will appear.
Type the following commands in the console:
% set ins [atomselect top protein]
% $ins writepdb insp.pdb
It will create a new file, namely, insp.pdb.

3.1. 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 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.

3.1.1. Using Automatic PSF builder

In the main VMD window, go to Extensions –> Modeling –> Automatic PSF Builder.
A new window will appear, namely, “AutoPSF” as shown below (Fig. 1):

Fig.1 Automatic PSF Builder in VMD.
Select the molecule insp.pdb in step 1.
It will show some topology files. Click ‘Load input files’.
In step 2., You can either select protein or everything or any other option based on your protein. Here, I am selecting ‘everything’.
Click ‘Guess and split chains using current selection’.
In step 3., click ‘Create chains’.
In step 4., click ‘Apply patches and finish PSF/PDB’.

3.1.2. 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.

References

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 physics, 153(4).
Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: visual molecular dynamics. Journal of molecular graphics, 14(1), 33-38.