[gmx-developers] How to name ions?

Berk Hess hess at cbr.su.se
Wed Jul 28 11:16:48 CEST 2010


While checking the last details of the Amber and Charmm force fields in
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.


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