Post date: Sep 12, 2011 9:55:59 AM

Yesterday night I've been playing with GROMACS as an attempt to find out how well would it go along with structures prepared for other software. There are still some grey areas, at least for me:

  • How does one parametrize ligands?
  • Are acetylated, n-methyl, methyl termini supported? PDB2GMX only offers a choice for the charged/uncharged variants (those which depend on pH).
  • How does one parametrize non-standard residues?
  • Variant FF for phophorylated residues: parametrization and mixing with newer versions of the FF are unclear.