Desmond Tutorial

Desmond Tutorial
Desmond Tutorial
Steps to Perform Simulation on a Simple Protein
While the example described in this tutorial is a basic simulation on a single protein, the
exercise is useful for learning the Maestro‐Desmond environment as well as, in general,
investigating the molecular properties of different proteins.
Preparing a molecular model for simulation involves these general steps:
1. Import a structure file into Maestro.
2. Prepare the structure file for simulation. During this step, you remove ions and molecules
which are artifacts of crystallization, set correct bond orders, add hydrogens,
detect disulfide bonds, and fill in missing side chains or whole residues as necessary.
3. Refine the prepared structure file. During this step, you analyze the choices made by
Maestroʹs Protein Preparation Wizard and manually change protonation and tautomeric
states of variable residues, and (when present) of ligands and co‐factors.
4. If your system is a membrane protein, immerse the protein in the membrane.
5. Generate a solvated system for simulation.
6. Distribute positive or negative counter ions to neutralize the system, and introduce
additional ions to set the desired ionic strength (when necessary).
7. Let Maestro assign OPLS‐AA force field parameters to the entire molecular system;
alternatively, assign force field parameters external to Maestro with Desmondʹs
Viparr utility program, which provides access to a variety of widely used force fields.
8. Configure simulation parameters using the Desmond window in Maestro or edit the
Desmond conguration file.
9. Run the simulation from Maestro or from the command line.
10. Analyze your results using the Trajectory Viewer and other analysis tools.
This process is illustrated in Figure 1.1.
2 D. E. Shaw Research September 2008