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.

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

1. Manual method
2. 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.

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

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Further Reading

Energy minimization and equilibration of simple protein using NAMD & VMD.

Tutorial: A quick MD simulation using NAMD and VMD

How to install VMD on Ubuntu?