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Molecular Modeling Practical

This tutorial introduces the student to the practice of Molecular Dynamics (MD) simulations of proteins. The protocol used is a suitable starting point for investigation of proteins, provided that the system does not contain non-standard groups. At the end of the tutorial, the student should know the steps involved in setting up and running a simulation, including some reflection on the choices made at different stages. Besides, the student should know how to perform quality assurance checks on the simulation results and have a feel for methods of analysis to retrieve information.

Introduction and Outline

The aim of this tutorial is to investigate differences in the conformation and dynamics of Prion Proteins (PrP) from different animal species. At the end of the tutorial the student should be able to:

  • Set up and run Molecular Dynamics Simulations of proteins using Gromacs
  • Perform quality assurance checks and analysis on simulation results
  • Compare simulation results obtained from different simulations

For this tutorial, students are expected to team up in groups of four. Each group will perform simulations on four Prion Proteins, thus each member of each group chooses one protein as the subject of the tutorial. At the end of the tutorial, the results from all four simulations will be combined.

Each group of students should write a report of no more than six pages, reflecting on the purpose of the work and the results obtained. In addition, specific questions are given, which have to be answered in the report. A description of the report, what it should contain and which questions are to be answered, is given on the report page. In the text, questions and assigments are indicated by grey boxes, like the following:

Write down your name and those of the members of your group

Commands are given in white on a blue background. These have to be typed carefully, since the shell (the program parsing the commands) is case-sensitive. A common error that may occur is replacing a 0 (digit zero) for an O (capital letter O), an l (lower case letter l) for a 1 (digit one), or vice-versa. You might want to copy-paste the commands, which is as simple as selecting them with the mouse and pressing the middle mouse button on the spot where the command should be entered. Now first try the following commands:


This lists your current user name. Make sure you're not logged in as "root".

ls -l

This gives a listing of the things that are in the directory where you are. Use this if you encounter errors like "file not found".


This command shows you the full path of the directory where you are.

Mind that copy-pasting does not relief you from reading the text! You can't run the tutorial without the instructions around the commands. It is naively assumed that the intention of the one following the tutorial is to learn something. In some cases you might be reminded to read carefully, by a comment like the following:

Read carefully!

Prion Proteins

Prion Proteins are expressed on the cell surface and are involved in copper binding, although their exact function is still unclear. Specific misfoldings of these proteins create prions (PRoteinaceous and Infectious, added extension -on), which can induce misfolding themselves and thus propagate the condition. The misfolded proteins aggregate and cause severe and fatal neurodegenerative disorders, such as Creutzfeld-Jakob Disease (CJD) in humans, Bovine Spongiform Encephalopathy (BSE) in cows (mad cow disease) and scrapie in sheep. Misfolding can occur due to mutations or due to infection with prions from food sources.

Full length human PrP is a 253 amino acid protein. The structure of PrP has been solved by NMR and by X-ray crystallography and is characterized by an N-terminal flexible region preceding a globular domain containing three alpha helices, forming an orthogonal bundle. The structure of the globular domain has been solved by NMR for many different animal species, including cow, sheep, elk, hamster, chicken, turtle and frog. Interestingly, these animals display different susceptibilities to prion disease, which may be connected to differences in the dynamics of the protein.

To investigate whether different forms of Prion Protein display different features in terms of conformation and dynamics, simulations will be performed on four of them and the results will be compared to each other.

Molecular Dynamics

Classical molecular dynamics simulations use Newton's equations of motion to calculate trajectories of particles, starting from a defined configuration. For each particle in the system, the total force acting on it is calculated from the interactions with other particles, as described by the force field. The force divided by the mass of the particle gives the acceleration, which, together with the prior position and velocity, determines what the new position will be after a small time step. The high spatial and temporal resolution make molecular dynamics simulations useful for testing models based on experimental data, for understanding principles underlying the function and to formulate new hypotheses. Unfortunately, system sizes are limited, as are time scales.


This tutorial uses Gromacs ( for performing and analysing molecular dynamics simulations. Gromacs is a suite of programs which is freely available under the GNU GPL (General Public License). The programs have a command-line interface, which means that each step involves typing the name of the program and a number of arguments. Note that the commands are case sensitive and each command has to be typed exactly as in the tutorial. More information about Gromacs as well as the manual can be found on the web site.


Since the programs have a command-line interface, there is no escape from using a terminal. Although it is possible to run Gromacs under Windows in a DOS terminal, there are several benefits attached to using Linux, which is the choice for this tutorial. For some students the transfer to Linux from Windows will form an obstacle as they are much used to the interface Windows offers. It is important to note that Linux is not intended to be a free clone of Windows. It is a powerful, highly costumizable operating system, which allows one to get much more performance from a computer. The transfer from Windows to Linux is sometimes described as switching from a motor cycle to a car. To start using the Linux terminal, it is necessary to know the most basic commands ( ls,cd,mkdir,cp,mv,rm,more). Some more information about linux/unix can be found here and here. A reference card (cheat sheet) can be found here

Starting structures and visualization

Before anything else, starting structures have to be obtained. These can be retrieved from the Protein Databank, which is a repository for three dimensional structures of proteins. It contains approximately 40 structures of prion proteins on a total of over 50000 structures. To start the tutorial, download the structures with ID's 1qlz, 1xyw, 1u3m, and 1xu0 from the database. Each student in a group of four can select one of these to use as the subject of the tutorial.

Check whether the downloaded structure is in fact a Prion Protein; Don't mistake 1qlz for 1q1z or 1xuo for 1xu0.

For each structure, write down the animal species it comes from.

Now first have a look at the structure in a molecular viewer. The following instructions are for Pymol, which should be available on your machine. Load the structures in Pymol using

pymol *.pdb

Now Pymol should start and a window should appear showing the structures in line representation. The models are listed on the right side of the main window and can be removed from view by clicking on the name. Next to each model name are menus which allow changing the representation. Try to show the structures as cartoons and color each chain with rainbow colors from N- to C-terminus. For those inclined to use a keyboard, which is strongly encouraged, the above can also be achieved by typing in the window:

disable 1qlz

(turn structure 1qlz off)

enable 1qlz

(turn the structue back on)

hide everything, all

show cartoon, all

spectrum count, rainbow, 1qlz

To get a better view of the structural homology, fit each structure onto the human form (1qlz). This can be done using the command 'align'. To align structure 1xyw onto 1qlz type:

align 1xyw, 1qlz

Note the similarities and dissimilarities between the different models. To see the differences better, it may be necessary to give each model a separate color again. Try zooming in on regions which are different and look at specific residues. You can change the representation of parts of a molecule by right-clicking on the chain. If you like the image you have, you can further improve it by typing 'ray' and save the resulting picture using 'png filename' to have a lasting memory of this tutorial.

Save an image of the aligned structures for the report

Now exit Pymol using the command 'quit'. As you may have noticed, all the information necessary to draw the structures is in the respective .pdb files. Have a look at the file using the command 'less' and try to understand the file format. 'less' is somewhat like 'more', but allows more control. The space bar and 'b' scroll forward and backward respectively, and with 'g' and 'G', you can go all the way to the top or to the end.
The PDB file contains a lot of information regarding the protein, the experimental methods used, conditions, etc. It also contains a listing of each atom with the Cartesian coordinates. Note that there is no information in the file regarding bonding, whereas Pymol, as most molecular viewers do, did draw bonds between atoms. These bonds were inferred from the interatomic distances.


To get started, make a directory for each of the structures. As results may be combined in the end, use a self-explanatory and unique directory name by combining the PDB id (1qlz, 1xyw, 1u3m, or 1xu0) with a group or personal identifier (e.g. group number or student name). Copy the structure file into the directory and change the directory. Student Pietje Puk, performing simulations on the human form 1qlz could, for example, type:

mkdir 1qlz_pietje_puk

cp 1qlz.pdb 1qlz_pietje_puk/

cd 1qlz_pietje_puk

Now it's time to start with the real Molecular Dynamics part. Remember to fill in the right filenames at every stage. In particular, the tutorial simply refers to "protein.pdb" and "protein-EM-solvated.gro", as generic names, which should be replaced with names specific to your protein (e.g. "1qlz.pdb" and "1qlz-EM-solvated.gro"). HINT: Rename your protein "protein.pdb" and you can simply copy-paste all commands. Be sure to read carefully and to check at each step whether it was successful. Read the output! In case a program gives an error message, it is usually self-explanatory. Check file formats and program output to understand the processes at each step. Most of the files are readable, except for files ending in .tpr, .xtc, .trr and .edr.

If you feel ready, click here to proceed.