LEaP will automatically add hydrogen atoms. In the 3MP9 structure, which was obtained using X-ray crystallography, hydrogen atoms are not resolved. In such case not B (namely A) should be chosen. The phrase and not altloc B refers to cases such as Thr25 or Glu50, in which the side-chain has two possible orientations. In the commands presented below, we use VMD to select chain A of the protein and write it out as proa.pdb. Using PDB ID: 3MP9 as an example, we show how to create prmtop and crd files for a protein composed of a single chain. In order to keep an uncluttered environment, execute the commands for each section inside the sections’s directory. $ mkdir Sec1 Sec2 Sec3 Sec4.1 Sec4.2 Sec5 Sec6 Sec7 Sec8Ī large number of files will be created during the execution of the following tutorial. $ echo "tutorial-5.2: Creating input files for AMBER" > README This tutorial consists of 8 sections, create a directory for each section. The name of the Amber path depends on your installation method. source /home/user/AMBER/amber21/amber.shĮxport AMBERHOME="/home/user/AMBER/amber21" Or alternatively, execute the commands directly in the command line. bash_profile file with respect to your installation path. First, download the program from the webpage. Of course, you can use the latest version of AmberTools. In this tutorial, we use AmberTools21, which is available free of charge. crd files produced in this tutorial can be used as input for GENESIS. In this tutorial, we use tleap, but the same procedures can also be performed using xleap. The former is a command-based tool to be used in a terminal, while the latter is an X Windows system tool for performing modeling in GUI. There are two tools in LEaP, tleap and xleap. Throughout this tutorial, we use the LEaP program, which is included in AMBER Tools, therefore before beginning this tutorial the user should install the latest version of AMBER Tools and set the environment for executing the LEaP program. In this tutorial, we provide a guide for preparing parameter files, topology files ( prmtop file), and coordinate files ( crd file) for running an MD simulation using the AMBER force field. 3. Changing the protonation states of side-chains
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