Dr. Henry Jakubowski
Molecular Modeling Programs: Chime, SpdbV, VMD, and NAMD
We will use a variety of molecular modeling programs to visualize complex biomolecule and systems of molecules and to calculate their properties. New programs are continually becoming available. After much thought, I have selected the following programs for use in the class.
1. Jmol: This is a programs that allows visualization of molecules and molecular systems using a web browser. It can run on any machine the runs Java, including PCs, MACs, Unix, and Linux computers. Its biggest use is in the creation of interactive, web-based tutorials to explain structure/function properties of molecules. Coordinates for proteins and nucleic acids (PDB format) can be obtained from the PROTEIN DATA BANK and the molecules displayed using Jmol. Molecules can be displayed in a variety of ways, including line, ball and stick, van der Waals, cartoon dot surfaces, and electrostatic surfaces You will develop a Jmol tutorials for a final project. A chief disadvantage is that the program can not perform energy minimization and dynamics calculations.
2. Chime: This is a programs that allows visualization of molecules and molecular systems using a web browser. The advantage of this program is that it is available as a free plug-in for Internet Explorer from MDI Systems, Inc. Its biggest use is in the creation of interactive, web-based tutorials to explain structure/function properties of molecules. Coordinates for proteins and nucleic acids (PDB format) can be obtained from the PROTEIN DATA BANK and the molecules displayed using Chime. Molecules can be displayed in a variety of ways, including line, ball and stick, van der Waals, cartoon dot surfaces, and electrostatic surfaces. A chief disadvantage is that the program can not perform energy minimization and dynamics calculations.
3. SpdbV: Deep View/Swiss-Pdb Viewer, is a free visualization program distributed by GlaxoSmithKline. T his program offers many advantages over Jmol and Chime. It can display several pdb files simultaneously, and can align the structures of different homologous proteins. The alignment can be based on individual residues, the main chain, or the entire proteins. RMS deviations of the aligned structures can be calculated. It can be used in conjunction with computer programs available at ExPASy (Expert Protein Analysis System) server in Geneva, Switzerland. A protein of known primary sequence but unknown tertiary sequence can be submitted through SpdbV to ExPASy, and by email, homologous proteins of known structures will be returned, which can serve as a guide to creating a modeling 3D structure of the unknown protein. For a given structure, new bonds, atoms, residues and loops can be added or removed. Surfaces (electrostatic, molecular) can be calculated. Energies can be calculated and minimized using the GROMOS96 force field and parameters. Nonbonded and bonded interactions energies are given in tables. You many need it for your final modeling project. It is available on the s: drive.
4. VMD (Visual Molecular Dynamics): VMD " is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer." It is available on the PC network (s drive). We will use this program for Lab 1 and can use it to display the results of molecular dynamics calculations using NAMD, which is described below. The program is available through the Theoretical Biophysics Group at: University of Illinois at Urbana-Champaign | Beckman Institute for Advanced Science and Technology
5 . NAMD (Scalable Molecular Dyanics): NAMD is a molecular dynamics code that can be run on the PC network and possibly on parallel cluster in the computer science department. We may use this program to run molecular dynamics simulations on selected molecular systems. The simulations will be viewed using VMD. NAMD is available on the s: drive.
Molecular Dynamics Tutorial from the Pittsburg Supercomputing Center
Flash Tutorials on use of the Protein Data Bank from the Protein Data Bank
Web Molecular Modeling Resources
MolVisOrg 3D Molecules
Charmm (Chemistry at Harvard for Molecular Mechanics): Molecular mechanics and dynamics simulations require a force field with parameters of the types of molecules that we will be studying. We will use predominately the Charmm force field. We probably wont' use Charmm in this course.
RTF files, param files:
Interpreting PDB files