[gmx-developers] How to name ions?
Rodrigo Faccioli
rodrigo_faccioli at uol.com.br
Wed Jul 28 17:56:39 CEST 2010
Hi,
First of all, sorry about my last email.
Berk, yes. My suggestion is issue 2).
In other words, in topology structure we can store what force-field was
selected in pdb2gmx. The user informs what ion he wants. Something like
--ion CL. If he didn't inform any ion, genion shows them.
The function what I mentioned I wrote below:
type_ions_t get_ion_id(char * ion_name){
if (strcmp(ion_name,"CL-")==0) {
return ionCL_
}else if (strcmp(ion_name,"CL")==0) {
return ionCL
}
enum type_ion {ionCL, ionCL_, ionNR}
typedef enum type_ion type_ion_t
Each force-field may has a structure to inform which ions id it works:
typedef struct sions_force_field{
type_ion type_ion_t
}ions_force_field_t
ions_force_field_t ions_charmm [] = { {ionCL}, {ionCL_}};
I hope that I wrote more clear my idea.
Thanks in advance,
--
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 12:05 PM, Ran Friedman <r.friedman at bioc.uzh.ch>wrote:
> 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 Bioinformaticshttp://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> <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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