Vmd atom selection by mass1/7/2024 ![]() We can see that it has deviated significantly from the origin (0, 0, 0). Now, we would like to also check the center of mass (COM) of the protein by using the “ measure center” command in VMD. In fact, these additional compounds were used for crystallization of the protein in the experiment, and are not essential for this MD simulation. We can find not only protein atoms but also oxygen of water and other compounds such as phosphate ion, isopropyl alcohol, and methylpentane diol. Let’s go to the “ 1_oripdb” directory, make a symbolic link to the PDB file, and look at the structure in VMD. We have already downloaded the PDB file in Tutorial 2.1. Here, we use the PDB ID: 2QMT, which was solved by X-ray crystallography at 1.05 Å resolution. Prepare the PDB file of the target protein toppar/Ġ0toppar_file_format.txt par_all36_cgenff.prm top_all35_ethers.rtfĪce par_all36_lipid.prm top_all36_carb.rtfĬheq par_all36_lipid_ljpme.prm top_all36_cgenff.rtfĭrude par_all36_na.prm top_all36_lipid.rtf # Check the contents in the symbolic link$ ls. topparġ_oripdb 2_modpdb 3_psfgen 4_solvate 5_ionize toppar # Make a symbolic link to the CHARMM toppar directory It is useful for referring to a directory or file that is far from the current working directory. Symbolic link is a kind of “shortcut” to the target. Here, we create a symbolic link to the directory where the CHARMM force field files are stored (see Tutorial 2.2) using the “ ln -s” command. In Step 3, we need CHARMM topology files. This is one of the effective techniques to keep the directories organized in MD simulation studies. 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 ( tutorial19-2.3.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. ![]()
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