Generating a Protein Structure File (PSF)

Of the four files mentioned above, an initial PDB file will typically be obtained through the Protein Data Bank, and the parameter and topology files for a given class of molecule may be obtained via the Internet at
http://www.pharmacy.umaryland.edu/$\sim$alex/research.html. The NAMD configuration file is created by the user. The PSF file, however, must be created by the user from the initial PDB and parameter files.

1

Go to the 1-1-build directory. In a Unix Terminal window, you can change directories using the cd command. Type cd 1-1-build. You can see the contents of the directory you are in by typing ls. In this folder, you will find many files that you will use later.

First, you will remove the water molecules from 1UBQ.pdb, and create a clean pdb file of the protein alone.

2

Open VMD by typing vmd in the Unix Terminal window, and load 1UBQ.pdb by clicking File $\rightarrow$ New Molecule... menu item in the VMD Main window. In the Molecule File Browser use the Browse... button to find the file 1UBQ.pdb. Load it by pressing the Load button.

Note that the x-ray structure from the Protein Data Bank does not contain the hydrogen atoms of ubiquitin. This is because x-ray crystallography usually cannot resolve hydrogen atoms. The pdb file you generate along with the psf will contain guessed coordinates for hydrogen atoms of the structure. Later, energy minimization of the protein will ensure their positions are reasonable.

3

Choose the Extensions $\rightarrow$ tkcon menu item and in the VMD TkCon window, type the following commands:

set ubq [atomselect top protein]
$ubq writepdb ubqp.pdb

(Hit the Return key after each command.)

In the previous step you have created the file ubqp.pdb, which contains the coordinates of the ubiquitin alone without hydrogens, in the 1-1-build directory.

4

Delete the current displayed molecule in VMD using the VMD Main window by clicking on 1UBQ.pdb in the window, and selecting Molecule $\rightarrow$ Delete Molecule. Close VMD by typing exit in the vmd console window.

5

Now, you will create the psf file of ubquitin. The psfgen package of VMD is very useful in this regard. In order to create a psf, you will first make a pgn file, which will be the target of psfgen. In a Unix Terminal window type nedit ubq.pgn to create a new file called ubq.pgn. (Be sure that you are in the 1-1-build directory.) Then, type the following lines:

package require psfgen
topology top_all27_prot_lipid.inp
alias residue HIS HSE
alias atom ILE CD1 CD
segment U {pdb ubqp.pdb}
coordpdb ubqp.pdb U
guesscoord
writepdb ubq.pdb
writepsf ubq.psf

6

After typing this, save the file by clicking File $\rightarrow$ Save and quit the text editor by clicking File $\rightarrow$ Exit.

The file you just created contains the necessary commands to create the psf file of ubiquitin with hydrogen atoms and without water. Each command of the pgn file is explained:

• Line 1: You will be running psfgen within VMD. This line requires that the psfgen package is available to be called by VMD.
• Line 2: Load the topology file top_all27_prot_lipid.inp
• Line 3: Change the residue name of histidine to the proper name found in the topology file. HSE is one of three names for histidine, based on the protonation state of its side group. See the science box below for more information.
• Line 4: The atom named ``CD1" ($\delta$ carbon) in isoleucine residues is renamed as ``CD", its proper name from the topology file. Since isoleucine contains only one $\delta$ carbon atom, the psf file does not use the number label after ``CD".
• Line 5: A segment called U is created, containing all atoms from ubqp.pdb. The segment command also adds hydrogen atoms.
• Line 6: Coordinates are read from ubqp.pdb and residue and atom names are matched. Old segment labels will be overridden with the new segment label ``U".
• Line 7: Coordinates of missing atoms (like hydrogens) are guessed based on residue definitions from the topology file.
• Line 8: A new pdb file with the complete coordinates of all atoms, including hydrogens, is written.
• Line 9: A psf file with the complete structural information of the protein is written.

7

In a Unix Terminal window (again, be sure that you are in the 1-1-build directory), type the following command: vmd -dispdev text -e ubq.pgn. This will run the package psfgen on the file ubq.pgn in the text only version of VMD (no graphics). It will generate the psf and the pdb file of ubiquitin with hydrogens.

In your screen you will see different messages. Warnings are related to the ends of your molecule and are normal. Your system should have 1231 atoms and 631 with guessed coordinates.

8

Close the text version of VMD by typing exit at the vmd > prompt.

Having run psfgen, two new files will now appear in your 1-1-build directory: ubq.pdb and ubq.psf. Check this by typing ls. You have created the psf! You may want to inspect ubq.pdb using nedit.

Figure 2: Flowchart indicating the role of files as used by VMD, NAMD, and psfgen.