Protein structure and visualizers. Any macromolecular visualizer can be used for viewing, altering and saving PDB files. We recommend Discovery studio Visualizer https://www.3dsbiovia.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php and/or Pymol Visulalizer https://pymol.org/2/ academic versions for optimal use. Although WebGro has internal tools that will clean up your protein file before starting simulations, we recommend users to inspect your protein file manually using Discovery studio Visualizer and save a clean copy of protein.pdb file. Please note: If you have missing side chain or missing atoms, simulation run could throw errors during preprocessing or during actual MD run. If you receive an email with empty results, please check your protein file for missing atoms or missing chain and fix it before submitting again. Step1: Go to WebGro protein simulation page here Step2:
