[gmx-users] Modifying the protein chain in GROMACS

[Tim Stauch]

Dear all,

I am currently trying to “mutate" a protein by changing its backbone directly, i.e. I am not interested in changing a specific amino acid against another (I’ve found out that you can use VMD or Pymol for this purpose), but I am rather interested in changing certain atoms in the backbone by another functional group. In other words, I would like to replace, e.g., the NH-C=O-CR unit of a certain amino acid by a couple of other atoms which do not comprise a peptide bond (e.g. a small aromatic ring). After this, I would like to run MD simulations.

How would I do this? Is this actually possible? I would really appreciate your help, because I have no idea how to do the first steps of setting up the calculation (generating an input file that pdb2gmx can read, etc.). Neither an extensive Google search nor the GROMACS manual were useful to me in this respect.

Best wishes,
Tim