GROMACS version: 2021
GROMACS modification: Yes/No
I have the include topology of my non-natural amino acid “aa-lig.itp” generated with Ligand Reader & Modeler. My goal is to add them to the CHARMM36 forcefield that I will use for my simulation.
From what I understand in the manual (Adding a Residue to a Force Field — GROMACS 2021.2 documentation) I should do as follow:
- Readjust the topologies obtained from the external generator, in this case, CHARMM-GUI, to the form required by the .rtp format.
Question n1: I have uploaded the .mol2 format coordinate to get the topologies without energy minimization. Would a minimization (e.g. with MMFF94s) of the non-natural amino acid before generating the topology be appropriate?
Question n2: Some differences are pretty clear between .itp and .rtp format. For example, in the former file the atom block contains an indexed atom type (N1, C1, C2, C3…), 8 columns whilst the latter doesn’t (N, C, CA, C3…) and it has only 4 columns. Does anyone know of a script like itptortp.py or perl for streamlining this step?
No new atom types are introduced apart for one covalent bond between the oxygen of my residue and the first atom of my inhibitor. Step 4 of the manual says "If you require any new bonded types, add them to
ffbonded.itp". Would this be my case then?
Add the residue to
residuetypes.datwith the appropriate specification (Protein, DNA, Ion, etc). Where is this file located? I have searched for the name of this file in the local installation directory but it is not there. Any clues?