Testing out your new residue

Now that you have the covalently bound substrate attached to the protein, let's try to simulate it. The first thing we need to do is create the .psf (protein structure file) and .pdb (protein data bank file) files we will need for the MD simulation. These files will be explained in the next few sections. For now, follow these instructions to use PSFGEN and make the necessary files.

Open a new terminal window and go to the directory:
> forcefield-tutorial/forcefield-files

This is where you have created your hisH_cyg_mod.pdb file. If not, move it into this directory now. Look at the contents of the directory by typing:
> ls

Note that we have provided you a topology file called top_all27_prot_na.inp; this is the normal CHARMM topology file distributed by the MacKerrell group. Here we will use it to build our .psf and .pdb files.

Also within this directory you will see a PSFGEN input file called build_covsub.pgn. At this point, we assume you are already familiar with PSFGEN (if not, please see the NAMD tutorial for more detailed explanations). Take some time to look at the file with a text editor, and read through all the lines in the file. The first line specifies which topology file we will be using, the next 3 lines specify alias commands, the next group of commands denotes the segname, any special start or end commands, and which pdb file to use to build the segment. More often than not, in simulations, you have many different segments in one huge pdb file, so it is common to see many grouping listing the different segments. Finally, we again specify which files will be used for the coordinates and the command guesscoord tells the program to build in any missing coordinates (hydrogens and any other atoms that might be missing). Lastly, it writes out the .pdb and .psf files.

At a prompt, type:
psfgen < build_covsub.pgn > myoutput

This command should take a few seconds to run. When it is finished, it will return the prompt.

When you tried running PSFGEN, it should have returned an error. To determine what the problem is, you need to read through the myoutput file. You can do this by typing the following at a unix prompt within the working directory:

> more myoutput

Now read through the myoutput file. You will see that there is a line that says:

unknown residue type CYG

You have made a new residue, but there is no information about a residue CYG in the standard topology file! Now you see why we need to build a topology file entry, as well as develop parameters for this novel residue. The rest of this tutorial will take you through some of the basics of doing this.