Collection of parameter files from Chipot and coworkers for NBFIX
terms for the additive CHARMM36 force field associated with cation-pi
and salt bridge interactions. Summary of files and detailed
description below. Citations are in the individual .prm files.

June 2024

Arg.prm: Added CAG atom type for central C in Arg: cation-pi
Tyr.prm: Added CAB atom type of carbons on aromatic ring of Tyr
para-cresol.prm: Added CG2R6B atom type for para-cresol, this is the model system for Try.prm
CHARMM36m-NBF.prm: cation-pi NBFIX, 
CHARMM36m-SBF.prm: salt-bridge NBFIX

Detailed description from Dr. Chipot, January 2024

I have been suggested to send you the attached files to be added to
the force field repository. These files contain the NBFIX's for
cation-π interactions, on the one hand, and salt-bridge interactions,
on the other hand, which have been determined from QM/MM free-energy
calculations (see

liu-et-al-2020-accurate-description-of-cation-π-interactions-in-proteins-with-a-nonpolarizable-force-field-at-no.pdf
liu-et-al-2021-accuracy-of-alternate-nonpolarizable-force-fields-for-the-determination-of-protein-ligand-binding.pdf
liu-et-al-2022-accurate-description-of-solvent-exposed-salt-bridges-with-a-non-polarizable-force-field-incorporating.pdf

As you will see in these papers, the NBFIX's really help compensate
the absence of induction effects and recover the correct energetics of
cation-π interactions.

The attached parameter files contain the NBFIX parameters for cation-π
and salt-bridge interactions with the CHARMM36m protein force field
and CHARMM general force field.  In our work, nine cation-π
interactions were studied, i.e., toluene, para-cresol, and
3-methyl-indole interacting with either ammonium, guanidinium, or
tetramethylammonium.  Additionally, we redefined atom types for
aromatic C of tyrosine/para-cresol (CHARMM36m protein/CGenFF), and
central C of arginine (CHARMM36m protein/CGenFF). CHARMM36m-NBF.prm
contains the NBFIX parameters for cation-π interactions between
phenylalanine, tryptophan-lysine/TMA (CHARMM36m protein-CHARMM36m
protein/CGenFF) also for toluene, 3-methyl-indole-NH4/TMA
(CGenFF-CGenFF). The NBFIX parameters describing cation-π interactions
between tyrosine/para-cresol/arginine with other groups are provided
in Tyr.prm, para-cresol.prm, and Arg.prm.  CHARMM36m-SBF.prm contains
all NBFIX parameters for salt-bridge interactions in the CHARMM36m
protein force field and CHARMM general force field.

