[gmx-developers] How to name ions?

Gerrit Groenhof ggroenh at gwdg.de
Wed Jul 28 12:03:20 CEST 2010


We can just decide on a scheme ourselves, can't we?

I propose to use

Cl (the chemical symbol) for the atomname, as this is also done for more
complex ions, like sulphate.
Cl- for the residue name, because that's what it is.
The type name we could use, in analogy to protein, chloride, so the full
name of the species.


Berk Hess wrote:
> Hi,
> While checking the last details of the Amber and Charmm force fields in
> Gromacs
> before the 4.5-beta release, I noticed naming inconsistensies.
> For an ion we have to choose the molecule type name, residue name and
> atom name
> (the atom type name is set by the force field). Currently different
> force fields in Gromacs
> use different naming schemes, for instance: CL, Cl, Cl-
> Also the user somehow needs to know these names when running genion.
> My question is if there is a best choice for these names.
> Maybe some force fields have names for this?
> Is there a pdb or IUPAC standard (I guess this is capitalized without
> the sign)?
> It would be convenient if all force fields use the same naming scheme.
> Berk

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