[gmx-developers] How to name ions?

[Ran Friedman]

Hi,

I'm in favour of the second (simpler) option and (following the
discussion) suggest to have the same convention used in PDB files - atom
and residue names without the charge and in capital letters (e.g., ZN).
This will also eventually enable dealing with them using pdb2gmx (on
most cases, see below).

Problems:
(1) Some atom names will be the same as in amino acids, e.g., CD
(cadmium) and CA (calcium). This is a minor issue in my opinion but
users should be aware of this because it may influence selections.
(2) How to deal with transition metals that have multiple oxidation
states. For this I suggest to have the most common state as the default
and other state with different residue name, e.g., CU for Cu2+ and CU1
for Cu+. There are not too many cases like this for ions where FF
parameters are commonly available I guess. pdb2gmx may ask the user
explicitly how to deal with such ions.

Thanks,
Ran

Berk Hess wrote:
> 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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>>
>>
>>     
>
>   


-- 
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: r.friedman at bioc.uzh.ch
Skype: ran.friedman
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