[gmx-developers] How to name ions?

[Rodrigo Faccioli]

Hi,

I would like to suggest use of enum for it. Example: In gromacs is created a
enum for showing all gromacs' ions. So, we build a function that receives a
char and returns its enum.

All gromacs routines work with that enum. This implementation guarantees a
pattern for gromacs routines which are apart of any force-field.

I've developed something like this. In [1] I show my enum that was created.

[1]
http://gitorious.org/protpred-gromacs/protpred-gromacs/blobs/master/include/enums.h



--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Wed, Jul 28, 2010 at 7:29 AM, Berk Hess <hess at cbr.su.se> wrote:

> 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
> > 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
> >>
> >>
> >>
> >
> >
>
> --
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20100728/4931fdb5/attachment.html>