[gmx-developers] How to name ions?

[Berk Hess]

Hi,

I don't understand your mail.

The are essentially two issues:
1) What molecule, residue and atom names should the ions have in the
force field files in Gromacs
2) How does the user know what names to use in genion.

Is your suggestion for issue 2)?

A proper solution would let genion print a list of ions or translate
standard ion names
to forcefield names. But that would require that genion knows which
force field you are using.
The simplest solution would be to use the same names for all force
fields and document
them in the manual.

Berk

Rodrigo Faccioli wrote:
> 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
> <mailto: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
>     >>
>     >>
>     >>
>     >
>     >
>
>     --
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