Therefore, we create a directory for each step and work “sequentially” in each directory. Such situation can lead to accidental mistakes. In fact, we will obtain multiple output files at each step, and if we do all the work in one directory, it will be difficult to recognize which file was output in which step. We have prepared these five directories to carry out each step. # Download the tutorial fileġ_oripdb 2_modpdb 3_psfgen 4_solvate 5_ionize When you unzip the file, you can see that there are five directories “ 1_oripdb“, “ 2_modpdb“, “ 3_psfgen“, “ 4_solvate“, and “ 5_ionize“, each of which corresponds to each step in the above figure. Let’s download the tutorial file ( tutorial22-2.3.zip). We will also use psfgen-plugin, solvate-plugin, and autoionize-plugin in VMD. Since GENESIS is not providing a structure setup tool, we will use VMD for this purpose. Here, we select Protein G as an example, and solvate the protein in 150 mM NaCl solution. The scheme consists of five steps: 1) prepare the PDB file, 2) remove unnecessary molecules from the PDB and move the center of mass (COM) of the protein to the origin, 3) add hydrogen atoms to heavy atoms, 4) place water molecules around the protein, and 5) randomly place ions in the water. The figure below outlines a general scheme for building a system for soluble proteins. This tutorial describes how to set up a system for all-atom MD simulations using the CHARMM force field. Prepare the PDB file of the target protein
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