param-file “system_setup_psf”: Protein structure file generated by the setup tool.param-file “system_setup_crd”: Coordinate file generated by the setup tool.Run Energy Minimizer tool with the following parameters: generate reference structures for restraints in NAMD (if selected).Set up periodic boundaries and generate Particle Mesh Ewald (PME).Minimise energy using a steepest descent algorithm followed by Adopted Newton Raphson (using the defined number of steps).This relaxes the system, removing any steric clashes or unusual geometry which could artificially raise the energy. Now, we need to perform energy minimisation. In addition, we have a PRM file which defines the parameters of the unit cell. The setup provides us with the CRD and PSF files needed to perform a simulation. “Custom topology and parameter files for ligands” (optional).“Buffer”: Edge to edge distance between the protein and the edge of the water box in angstroms.param-file “crd input”: Coordinate file of the protein-ligand system.param-file “psf input”: Protein structure file of the protein-ligand system. Run System Setup tool with the following parameters: The entire workflow (preparation + simulation) is shown below for CHARMM and NAMD. The workflow method is most efficient and the individual tools used in the workflows are discussed below. The process can be accomplished by selecting each tool from the tools menu, or by importing the workflow. If you already completed the Setting up molecular systems tutorial, which covers the use of the CHARMM graphical user interface (GUI), you have already prepared your system, so go straight to the second section, using the files you prepared earlier. In the second section, we will perform an equilibration and production simulation, using NAMD. In the first section, we will look at preparation of a system (solvation, charge neutralisation, energy minimisation) using CHARMM. If you are interested in following this tutorial, you will need to download the BRIDGE docker container and download NAMD yourself. Please note NAMD tools are not currently available on a public Galaxy server due to licensing issues. In this tutorial we will perform a simulation with the popular NAMD molecular dynamics software.
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