精品文档---下载后可任意编辑Lysozyme in WaterJustin LemkulDepartment of Biochemistry, Virginia TechThis example will guide a new user through the process of setting up a simulation system containing a protein (lysozyme) in a box of water, with ions. Each step will contain an explanation of input and output, using typical settings for general use.This tutorial assumes you are using a GROMACS version in the 4.5.x series.GROMACS TutorialStep One: Prepare the TopologyWe must download the protein structure file we will be working with. For this tutorial, we will utilize hen egg white lysozyme (PDB code 1AKI). Go to the RCSB website and download the PDB text for the crystal structure.Once you have downloaded the structure, you can visualize the structure using a viewing program such as VMD, Chimera, PyMOL, etc. Once you've had a look at the molecule, you are going to want to strip out the crystal waters. Use a plain text editor like vi, emacs (Linux/Mac), or Notepad (Windows). Do not use word processing software! Delete the lines corresponding to these molecules (residue "HOH" in the PDB file). Note that such a procedure is not universally appropriate (i.e., the case of a bound active site water molecule). For our intentions here, we do not need crystal water.Always check your .pdb file for entries listed under the comment MISSING, as these entries indicate either atoms or whole residues that are not present in the crystal structure. Terminal regions may be absent, and may not present a problem for dynamics. Incomplete internal sequences or any amino acid residues that have missing atoms will cause pdb2gmx to fail. These missing atoms/residues must be modeled in using other software packages. Also not...
