[gmx-users] About peptide mutation with non-standard residue

[Chris Neale]

Dear Vicente:

If you can build your own hydrogen atom coordinates in your modified
residue, then I suggest that you look at the lysine entry in the .rtp file
in your force field directory, copy it, and modify it to match your
modified amino acid. This will have a different location based on your
force field, but for amber99 it would be here:
share/gromacs/top/amber99.ff/aminoacids.rtp

Then, you need to modify share/gromacs/top/residuetypes.dat so that it
includes your amino acid name as a Protein residue.

That should allow you to run gmx pdb2gmx with an input of a regular protein
structure and get a .itp file for your protein with the modified residue.

If you need gromacs to add hydrogens for you, then that will require also
modifying the forcefield .hdb file(s), but it sounds like you might already
have that under control.

Good luck, this is straightforward but reasonably tricky.
Chris.