Step One: Prepare the Protein Topology
We must download the protein structure file we will be working with. For this tutorial, we will utilize T4 lysozyme L99A/M102Q (PDB code 3HTB). Go to the RCSB website and download the PDB text for the crystal structure.
Once you have downloaded the structure, you can visualize it 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, PO4, and BME. 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 or other ligands. We will instead focus on the ligand called "JZ4."
If you want a cleaned version of the .pdb file to check your work, you can download it here. The problem we now face is that the JZ4 ligand is not a recognized entity in any of the force fields provided with GROMACS, so pdb2gmx will give a fatal error if you were try to pass this file through it. Topologies can only be assembled automatically if an entry for a building block is present in the .rtp file for the force field. Since this is not the case, we will prepare our system topology in two steps:
Since we will be preparing these two topologies separately, we must move the protein and JZ4 into separate coordinate files. Save the JZ4 coordinates like so:
grep JZ4 3HTB_clean.pdb > JZ4.pdb
Then simply delete the JZ4 lines from 3HTB_clean.pdb. At this point, preparing the protein topology is trivial. There are no missing atoms or residues in the 3HTB structure, so simply run pdb2gmx:
gmx pdb2gmx -f 3HTB_clean.pdb -o 3HTB_processed.gro -water spc
The structure will be processed by pdb2gmx, and you will be prompted to choose a force field:
Select the Force Field: From '/usr/local/gromacs/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9) 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
For this tutorial, we will use the united-atom GROMOS96 43A1 force field, so type 9 at the command prompt, followed by 'Enter'.
Bevan Lab Homepage
Virginia Tech Homepage
Virginia Tech Biochemistry
Site design and content copyright 2008-2015 by Justin Lemkul
Problems with the site? Send them to the Webmaster