[gmx-developers] How to name ions?

Daniel Larsson larsson at xray.bmc.uu.se
Fri Aug 6 18:23:22 CEST 2010 

In 4.5b2 oplsaa.ff/ions.itp:

sodium is called 'NA+' (molecule type and residue name) while all the other ions has it w/o sign.



On Jul 28, 2010, at 17:56 , Rodrigo Faccioli wrote:

> 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 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
>>>     >>
>>>     >>
>>>     >>
>>>     >
>>>     >
>>> 
>>>     --
>>>     gmx-developers mailing list
>>>     
>>> gmx-developers at gromacs.org <mailto: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
>>> 
>>>     
>>> <mailto:gmx-developers-request at gromacs.org>
>>> .
>>> 
>>> 
>>>     
>>> 
>>   
> 
> 
> -- 
> ------------------------------------------------------
> 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
> ------------------------------------------------------
> 
> 
> --
> 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.
> 
> -- 
> 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.

More information about the gromacs.org_gmx-developers mailing list