[gmx-developers] How to name ions?

Berk Hess hess at cbr.su.se
Wed Jul 28 12:29:15 CEST 2010

Gerrit Groenhof wrote:
> Hi,
> We can just decide on a scheme ourselves, can't we?
Yes and no.
We somehow need to translate ions present in pdb files to molecule types,
residue names and atom names.
So to do everything consistently, we would need to add renaming schemes
(residue and atom renaming in pdb2gmx is fully supported in version 4.5).
> 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.
> Gerrit
But what about multivalent ions?
Cu2+? And then Cu+ or Cu1+?
Note that 4 characters strictly speaking do not fit into the pdb format.

> 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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