Gmx editconf -f protein.pdb -o boxed.pdb -c -d 1.0 -bt dodecahedron Edit the topol.top file generated for the protein to include the required files for the ligand.The jz4_ini.pdb file into the protein.pdb file, right after the last line for the protein.Ītoms will be automatically renumbered in the next step. Merge the protein and ligand coordinates, by inserting the ATOM lines from.It is not used in this simulation,Īnd should not be confused with the required topol.top file, the system topolgy file. The file, jz4.top, is a GROMACS prototype topology file which indicates where to place specific files for the protein and jz4 ligand. Three of the files, jz4.itp, jz4.prm, and jz4_ini.pdb are required GROMACS files for the ligand component of the protein-ligand complex. Jz4_ini.pdb - PDB file for the initial coordinates of the jz4 ligand Subsequently, the file jz4.str is now available for download, and can be used for both CHARMM and GROMACS.Ī separate python file, cgenff_charmm2gmx_py2.py, is required for converting a the CHARMM jz4.str file into GROMACS input files.Ĭgenff_charmm2gmx_py2.py jz4 jz4.mol2 jz4.str charmm36-mar2019.ff The jz4.mol2 is then submitted to the CGenFF server.` Convert the jz4.pdb file to a jz4.mol2 using Babel.Gmx pdb2gmx -f protein.pdb -ff charmm36-mar2019 -water tip3p -ignh -o conf.pdb -nochargegrp The Ligand Generate a GROMACS topology ( topol.top) for the protein, without the ligand.Separate the original pdb file into two pdb files, one for the protein and one for the small-molecule ligand, jz4. The following steps provide one way to obtain parameters for the small molecule organic ligand when the CHARMM force field is used. Parameters for the protein component are well-known and usually do not present any difficulty,īut parameters for the small organic molecule must be obtained from a different force field. Organic molecule that is within the protein.
The problem with a protein-ligand system is that the force field parameters, as well as other parameters, must be determined for both the protein and the small If a required file is needed in a subdirectory for use with the GROMACS command, copy that file to the subdirectory first. The workflow for this exercise is such that each step is carried out in order and inside the appropriate directory.Įach subdirectory depends on a specific task that is to be carried out, and is worked through in sequence.
analysis/ - different ways of analyzing the trajectory are described.production/ - perform a Molecular Dynamics simulation using GROMACS.equilibration2/ - perform an NPT equilibration using GROMACS.equilibration1/ - perform an NVT equilibration using GROMACS.posres/ - position restraints on the heavy protein atoms, allowing the solvent to equilibrate around the protein without disturbing the protein structure.ligand/ - CHARMM parameter and coordinate files in GROMACS format for the ligand.charmm36-mar2019.ff/ - CHARMM force field parameters.The following is a short description of the directories: Perform these different steps in separate directories in order toĪvoid overwriting files or using wrong files.įor this tutorial the suggested directory layout is the following: The workflow for setting up, running, and analysing a simulationĬonsists of multiple and rather different steps. There are several other important minor differences which will become obvious as the tutoral proceeds. The GROMACS ligand topology and parameter files are obtained from the CGenFF server.The CHARMM force field is used for both the protein and the ligand.This GROMACS tutorial mostly follows the Protein-Ligand Complex Tutorial atīy Justin A. GROMACS: MD Simulation of a Protein-Ligand Complex GROMACS: MD Simulation of a Protein-Ligand Complex
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