Properly including bromide in GROMOS96 54a7

[alevilla]

Hi,

@esmee

When I then tried to run the energy minimization step (following the Lysozyme tutorial) i got the error message “atomtype BR- not found”.

The reason is that you change the name from BR → BR- and BR- is not defined as atomtype in the force field files. Atom type information are storage in ffnonbonded.itp in the [ atomtypes ] directive and [ nonbond_params ] directive (for gromos force field) and in the database atomtypes.atp.
To know more on the format see https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html

@esmee

In atomtypes.atp I can see that there is bromine (non-ionic) present, which is denoted BR. Does this mean that when putting BR instead of BR- under “at type” in ions.itp, the parameters in e.g. ffnonbonded.itp for the neutral bromine are used also for the bromide?

yes.

@esmee

If so, is this an ok approach anyway (I can for example see that values in ffnonbonded.itp differ between entries for CL and CL-, which is my reason for doubting the approach)?

BR and BR- are different, it is more appropriate to describe them using different LJ parameters.

@esmee

If it is not an ok practice, how do I properly add BR-? Do I have to add it also to atomtypes.atp, and to add values for c6, c12 and nonbond_params in ffnonbonded (where does one obtain such values for bromide, if so)? Are there any other files of the gromos54a7 force field that have to be modified as well?

When you add a new ion, it is good to add it also in ions.itp.

\Alessandra