Psf file pdb

This includes connectivity, classical charge, and other things. What we need to do, essentially, is use the PDB file to specify the primary sequence of the protein. We will piece together the protein using the topology libraries from this sequence, like adding beads to a chain. This will generate the PSF file. There are a number of ways to do this. The two ways we will do it is through the tkcon, and a menu plugin, AutoPSF.

The general procedure here is: acquire a suitable protein strip out the protein from the water from the Put it in your main class directory so you can find it easily. Open up VMD and then a tkcon. We will use the small leucine zipper that we examined earlier. NOTE: for the most part, these lines should be entered as written here: after each line hit [return]. This is not always necessary, but it is good programming practice to keep one command per line. Remember that everything after the hash " " character is a comment and is not processed.

Notice there are no hydrogens! This is normal. More on this type of thing later. In general, ANY name can be used here, but it should be descriptive. It must be 4 letters or less. Notice the brackets—these brackets define the PSF generation. Notice that each record contains the residue type. The next data field contains the residue sequence number. Notice that as the residue changes from histidine to serine, the residue number changes from 1 to 2.

Two like residues may be adjacent to one another, so the residue number is important for distinguishing between them. The next three data fields contain the X, Y, and Z coordinate values, respectively. The last three fields shown are the occupancy, temperature factor B-factor , and element symbol. The spacing of the data fields is crucial. If a data field does not apply, it should be left blank. The TER record terminates the amino acid chain.

A more complicated protein, hemoglobin, consists of four amino acid chains, each with an associated heme group. There are two alpha chains identifiers A and C and two beta chains identifiers B and D.

Again, the extra oxygen atom OXT appears in the terminal carboxyl group. The TER record indicates the end of the peptide chain. It is important to have TER records at the end of peptide chains so a bond is not drawn from the end of one chain to the start of another.

In the example above, the TER record is correct and should be present, but the molecule chain would still be terminated at that point even without a TER record, because HETATM residues are not connected to other residues or to each other. If a data file fails to display correctly, it is sometimes difficult to determine where in the hundreds of lines of data the mistake occurred. It is important to notice that hydrogens are not added to the protein in this step because it will be done automatically by a VMD script to avoid issues with atom names differences.

On the other hand, for ligands, hydrogens are added using custom forcefield parameters explicitly. Run this code by using Chimera. Notice that the new matched pair automatically loaded. How can we compare to see if the new matched pair is exactly the same atoms, etc as the old one? There are two ways.

First, we can compare the two structures visually. This is OK, but probably not very satisfying. The other way is to perform an RMSD.

Dealing with Multiple chains Some proteins consist of symmetric pieces, so it is natural to treat these somehow are repeating units. However, similar to quantum numbers for multi-electron atoms, each atom in a simulation set must be uniquely identified. The answer to this is to make each symmetric piece a chain.

Everything about atoms in two separate chains can therefore be the same, except the chain ID. This means that larger proteins must have multiple chains, whether or not they can be broken up into clean, symmetrical units. Hydrogens can be stripped out and added back in with "guesscoord". You can then repeat this for Chain B. Making Multiple copies You can then repeat this for Chain B. Often your simulation system may have multiple copies of smaller molecules: the solvent usually some water model , lipids in a bilayer, sodium ions, etcetera.

In this exercise, we will create a simple arrangement of POPE phosphatidylethanolamine lipids. One lipid will be replicated into nine, and we will arrange them in a 3x3 LIP using tkcon. It will also serve to illustrate how to assign different segment IDs to the lipids. Segment names cannot be more than four characters, unfortunately. Assuming this is a new session, we will load psfgen and the topology file again. This will create nine lipids in the PSF, but to begin with they will all be stacked upon themselves.

They will be segment-labeled R11 through R13 three rows with three each. Since there is only one residue per segment, and that is a POPE molecule, that is all we ahve to say here.