Parametrization and Simulation with Generic Residues

step1: parametrize the residue

  1. copy the complete forcefield-folder (e.g.amber99sb-ildn.ff) and residuetypes.dat to your working directory (you can find the folder and the file in /usr/share/gromacs/top/)
  2. you have to change at least 3 files: residuetypes.dat, amber99sb-ildn.ff/aminoacids.rtp and amber99sb-ildn.ff/aminoacids.hdb
    to avoid problems - choose a res-name with 3 characters! correct spaces are important!!!
    problems!? -> ask google and the gromacs manual!

step2: create input files

  1. use pdb2gmx in your working directory to create and input_min.pdb (see Tutorial "Protein-stability...")
    DON`T skip the minimization or be sure to have a minimized structure. Otherwise babel is not able to create the correct bonds and you will get a lot of subunits and wrong energies!!
    1 pdb2gmx -f -ignh protein.pdb -o input_min.pdb -water none -ff amber99sb-ildn
  2. convert these files to epqr and dh and rename the termini:
    1 python ~\poempp\python\ --rename-termini conf.gro
    -> topol.epqr and topol.epqr.dh
    the termini with name XYZ are renamed to NXY (N-terminus) and CXY (C-terminus)
  3. convert the epqr to mol2
    1 babel -i pqr topol.epqr -o mol2 topol.mol2
  4. create a spf-file:
    open simonagui and go to "Settings/Tools"
    select "only use bond information from input file"
    • choose the mol2 file in the bottom file menu and click "add molecule" (topol.mol2)
    • right click on residues and choose "generate parameter with" -> "epqr" and select te epqr (topol.epqr) and click "open"
    • right click on structure and choose "read inter-residue bonds/moves from molecule file" and select the mol2 (topol.mol2) and click "open"
    • set the spf path in the top file menu and save the spf-file (protein.spf)
  5. create the xml-file:
    go to "Generic Monte Carlo" in the main menu of the simonagui
    • set the mol2 as "Input Configuration" (topol.mol2)
    • choose the "Output xml" name (protein.xml)
    • set the spf as "Parameter file" (protein.spf)
    • choose the forcfield terms
    • "Gromacs dihedral potential":be sure to set the right path/filname for the dihedral file (topol.epqr.dh)!