Molecular Dynamics Simulation of Micromolecules using Chimera
Performing a Molecular Dynamics (MD) simulation of a small molecule in UCSF Chimera involves a series of steps to prepare the molecule, set up the simulation environment, run the simulation, and finally, analyze the resulting trajectory. Here's a step-by-step guide based on the information provided: 1. Loading and Preparing the Small Molecule Structure Open Chimera: Launch UCSF Chimera or ChimeraX. Load your molecule: Import your small molecule structure into Chimera using File > Open or File > Fetch by ID if the structure is available in a database like the Protein Data Bank (PDB). Add Hydrogens: Use the "Molecular Dynamics Simulation" tool's "Prep Structure" section to add hydrogens. You might also be able to use the addh command. Assign Force Field Parameters: Since you are working with a small molecule (a nonstandard residue), you will use Amber's Antechamber module, which is included in Chimera, to assign force field paramete...