Adding a Residue to a Force Field

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    Version as of 07:38, 2 Dec 2021

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    If you have the need to introduce a new residue into an existing force field, there are several files you will need to modify.  Follow these steps:

    1. Add the residue in the .rtp file for your chosen force field.
    2. If you need hydrogens 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.


    In GROMACS 4.5 and later, this is best done by making a full copy of the installed forcefield directory (e.g. $GMXLIB/amber99sb.ff) and residuetypes.dat into your local working directory. 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.

    Page last modified 04:40, 19 Mar 2011 by mabraham