Informational and File Sharing Server

Modeling of Macromolecular Systems

Home

Tutorials

Share

Tutorial 2: Including ligands in protein simulation

Basic instructions

You may want to include ligands in your protein simulation (such as cofactor, substrate or inhibitor). In this case you should load extra ligand.lib (atom types, charges and connectivity) and ligand.frcmod (additional force field parameters) files into tleap. Notice, that atomic names and atomic order in the input protein_lig.pdb file must be the same as in ligand.lib.

let's assume that your protein structure contains bound cofactor and substrate. First of all you should inspect Amber parameter database and RESP ESP charge DDataBase for your ligand. Let`s suppose that you`ve found parameters for cofactor but failed with substrate. So you only need to parametrize your substrate (see next section). Once all necessary files are prepared you could load them in tleap to allow inclusion of ligands in your system:

next