Building a Model System for Desmond Simulations

Performing simulations on aqueous biological systems requires the preparation of biological molecules such as proteins and ligands, addition of counter ions to neutralize the system, selection of simulation box size, solvation of the solutes using explicit solvent molecules, and alignment of proteins to a membrane bilayer (if used). This procedure is often tedious if it has to be performed manually. Tools for all these tasks are provided with Maestro.

Protein and ligand structures used in a Desmond simulation must be complete all-atom 3D structures with a reasonable geometry. The preparation of protein and ligand structures for use in a simulation can be done with the Protein Preparation Wizard and LigPrep. The Protein Preparation Wizard corrects structural defects, adds hydrogen atoms, assigns bond orders, and can selectively assign tautomerization and ionization states, and optimize the hydrogen bonding network. For more information, see the Protein Preparation Guide — Contents. LigPrep performs 2D-to-3D conversion if necessary, adds hydrogen atoms, generates tautomers, ionization states, ring conformations, and stereoisomers, as requested, and produces minimized 3D structures. For more information, see the LigPrep User Manual — Contents.

Once you have prepared the protein and ligand structures, you can proceed to the remaining tasks in building a model system that can include proteins, ligands, explicit solvent, a membrane, and counter ions. The System Builder automates this process and significantly reduces the effort required. You can set up and run a System Builder job from the System Builder Panel, or from the command line (see Preparing Desmond Systems). System Builder jobs can be run on Linux, Mac, or Windows platforms, in contrast to Desmond simulations, which only run on Linux.

To open this panel, do one of the following:

• Click the Tasks button and browse to Classical Simulation → System Setup
• Click the Tasks button and browse to Desmond → System Builder
• Click the Tasks button and browse to Biologics → Molecular Dynamics → System Setup
• Click the Tasks button and browse to Materials → Classical Mechanics → More MD Tasks → System Builder

Before you start working in this panel, display the solutes in the Workspace.

Modifying and Rebuilding a Model System

If you want to modify an existing model system (i.e. a full system, containing all components), and run a simulation on it, you do not need to completely rebuild the system in the System Builder Panel. Instead, you can simply regenerate the model system. To do so, include the modified full model system in the Workspace, then choose click the Tasks button and browse to Classical Simulation → Model System Regeneration. A Job Settings dialog box opens, so you can specify the usual job parameters.