[gmx-developers] How to name ions?
hess at sbc.su.se
hess at sbc.su.se
Fri Aug 6 22:47:55 CEST 2010
Fixed.
Thanks for reporting this,
Berk
> 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.
>
> --
> 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