Introduction

Molecular dynamics (MD) simulations are a powerful scientific tool used to study a wide variety of systems in atomic detail. From a standard protein simulation, to the use of steered molecular dynamics (SMD), to modelling DNA-protein interactions, there are many useful applications. With the advent of massively parallel simulation code such as NAMD2, the limits of computational analysis are being pushed even further.

Inevitably there comes a time in any molecular modelling scientist's career when the need to simulate an entirely new molecule or ligand is necessary. Therefore the technique of determining new force field parameters to describe these novel system components becomes an invaluable skill. Determining the correct system parameters to use in conjunction with the chosen force field is only one important aspect of the process. Equivalently, the ability to use several programs simultaneously to examine and refine the system in question is also a critical element of these kinds of problems. However, it should be noted that the extent of parameterization carried out in this exercise is minimal and designed to emphasize the major points required in a more detailed fitting procedure. Road-maps for more systematic optimizations that include experimental data can be found in a series of articles for Charmm [1,2], Amber [3], and other force fields, including OPLS-AA [4,5] and ECEPP. Additional sources for parameterization can also be found on the web (see [6], [7], [8], [9]). Polarizable force fields that include terms to allow polarization of the charge distribution by environment are under development [10].

This tutorial will walk you through a comprehensive example of how one investigates, sets up, and simulates a small nonstandard ligand bound to a protein system; specifically, we will investigate the glutaminase subunit of the hisH-hisF system and will determine parameters for the nonstandard residue.

Starting from the crystal structure in the protein database, and using the breadth of available biochemical information, we will dock the small ligand (glutamine) to the active site of hisH and develop the missing parameters in accordance with the Charmm22 force field. As a first guess for the parameters, we will try to derive as many of the missing parameters as possible from existing similar molecules already parameterized in the force field. Then we will further refine these new parameters with semi-empirical quantum chemistry calculations. Once the new parameters are finalized, we will minimize the system. The combination of all of these techniques will require the use of at least four different computational biology and chemistry packages.

The entire tutorial takes about 3 hours to complete.

This tutorial assumes that MOE [11], Spartan [12], VMD [13], NAMD [14] and other software has been correctly installed on your computer. All the necessary files must be copied over to a directory called tbss.work in your home directory. Go to this directory by typing:

tbss$>$cd $\sim$/tbss.work

Copy the needed directory, but instead of typing TOP_DIR, type the location of the Summer School directory tree:

tbss$>$cp -r TOP_DIR/sumschool03/tutorials/06-forcefield/data ./data

For instance, if the materials are located at /mnt/cdrom or at $\sim$/Desktop, replace TOP_DIR by /mnt/cdrom or $\sim$/Desktop. Use this copy of the tutorial files. Change your current directory to data by typing

tbss$>$cd $\sim$/tbss.work/data