Adding a Residue to a Force Field

Adding a new residue

If you have the need to introduce a new residue into an existing force field so that you can use pdb2gmx, or modify an existing one, there are several files you will need to modify. You must consult the manual for description of the required format. Follow these steps:

1. Add the residue to the .rtp file for your chosen force field. You might be able to copy an existing residue, rename it and modify it suitably, or you may need to use an external topology generation tool and adapt the results to the .rtp format.
2. If you need hydrogens to be able to be added to your residue, create an entry in the relevant .hdb file.
3. If you are introducing new atom types, add them to the atomtypes.atp and ffnonbonded.itp files.
4. If you require any new bonded types, add them to ffbonded.itp.
5. Add your residue to residuetypes.dat with the appropriate specification (Protein, DNA, Ion, etc).
6. If the residue involves special connectivity to other residues, update specbond.dat.

To avoid an issue with grompp, in your new residue do not use the atom names O1, O2, and probably H1, H2 and H3 also. These might otherwise be picked up as atoms from possible peptide termini, which is likely not what you'd want.

Note that if all you are doing is simulating some weird ligand in water, or some weird ligand with a normal protein, then the above is more work than generating a standalone .itp file containing a [moleculetype] (for example, by modifying the .top produced by some parameterization server), and inserting an #include of that .itp file into a .top generated for the system without that weird ligand.

Modifying a force field

In GROMACS 4.5 and later, modifying a force field is best done by making a full copy of the installed forcefield directory and residuetypes.dat into your local working directory:

cp -r $GMXLIB/residuetypes.dat $GMXLIB/amber99sb.ff .

Then, modify those local copies as above. pdb2gmx will then find both the original and modified version and you can choose the modified version interactively from the list, or if you use the pdb2gmx -ff option the local version will override the system version.