SIMONAPreprocessor
Protein stability - Simulations with PFF03

what you need:

  1. Gromacs on your computer
  2. Simona
  3. pdf of the protein (protein.pdb)
  4. mdp file for minimization with gromacs: http://intfolding/webfiles/Minimierung.mdp
  5. sml file to generate the xml file: http://intfolding/webfiles/amber99sb-ildn_prot_stab.sml

what to do:

  1. 1 pdb2gmx -f -ignh protein.pdb -o input_min.pdb -water none -ff amber99sb-ildn
    • if you want to skip the minimization type "-o conf.gro" instead of "-o input_min.pdb"
    • "-ignh": all hydrogens will be deleted and added with the right names according to the .hdb file in /usr/share/gromacs/top/amber99sb-ildn -> further informations:gromacs manual ;-)
    • "-ff amber99sb-ildn": you can also use amber99sb, but with amber99sb-ildn, you have additional dihedrals (also sidechain dihedrals..)
  2. 1 grompp -f Minimierung.mdp -c input_min.pdb
  3. 1 mdrun
    -> results in md.log
  4. 1 python ~/poempp/python/gromacs_to_epqr.py topol.top confout.gro protein.epqr
    if you skipped the minimization (step 2 and 3), you can use the conf.gro from step 1) instead the confout.gro from step 3)
  5. rename your dihedral file "mv protein.epqr.dh winkelfile.dh" or change the name of the dihedral-file in the sml!
  6. 1 python ~/poempp/python/SIMGenerateIdenticalRun.py amber99sb-ildn_prot_stab.sml protein.epqr protein.xml
  7. copy the xml file, change the temperatures and run your simulations!