Hi,<br><br>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.<br><br>All gromacs routines work with that enum. This implementation guarantees a pattern for gromacs routines which are apart of any force-field. <br>
<br>I've developed something like this. In [1] I show my enum that was created.<br><br>[1] <a href="http://gitorious.org/protpred-gromacs/protpred-gromacs/blobs/master/include/enums.h">http://gitorious.org/protpred-gromacs/protpred-gromacs/blobs/master/include/enums.h</a><br>
<br><br><br clear="all">--<br>Rodrigo Antonio Faccioli<br>Ph.D Student in Electrical Engineering<br>University of Sao Paulo - USP<br>Engineering School of Sao Carlos - EESC<br>Department of Electrical Engineering - SEL<br>
Intelligent System in Structure Bioinformatics<br><a href="http://laips.sel.eesc.usp.br">http://laips.sel.eesc.usp.br</a><br>Phone: 55 (16) 3373-9366 Ext 229<br>Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218">http://lattes.cnpq.br/1025157978990218</a><br>
Public Profile - <a href="http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5">http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5</a><br>
<br><br><div class="gmail_quote">On Wed, Jul 28, 2010 at 7:29 AM, Berk Hess <span dir="ltr"><<a href="mailto:hess@cbr.su.se">hess@cbr.su.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">Gerrit Groenhof wrote:<br>
> Hi,<br>
><br>
> We can just decide on a scheme ourselves, can't we?<br>
><br>
</div>Yes and no.<br>
We somehow need to translate ions present in pdb files to molecule types,<br>
residue names and atom names.<br>
So to do everything consistently, we would need to add renaming schemes<br>
(residue and atom renaming in pdb2gmx is fully supported in version 4.5).<br>
<div class="im">> I propose to use<br>
><br>
> Cl (the chemical symbol) for the atomname, as this is also done for more<br>
> complex ions, like sulphate.<br>
> Cl- for the residue name, because that's what it is.<br>
> The type name we could use, in analogy to protein, chloride, so the full<br>
> name of the species.<br>
><br>
> Gerrit<br>
><br>
><br>
</div>But what about multivalent ions?<br>
Cu2+? And then Cu+ or Cu1+?<br>
Note that 4 characters strictly speaking do not fit into the pdb format.<br>
<font color="#888888"><br>
Berk<br>
</font><div><div></div><div class="h5">> Berk Hess wrote:<br>
><br>
>> Hi,<br>
>><br>
>> While checking the last details of the Amber and Charmm force fields in<br>
>> Gromacs<br>
>> before the 4.5-beta release, I noticed naming inconsistensies.<br>
>> For an ion we have to choose the molecule type name, residue name and<br>
>> atom name<br>
>> (the atom type name is set by the force field). Currently different<br>
>> force fields in Gromacs<br>
>> use different naming schemes, for instance: CL, Cl, Cl-<br>
>> Also the user somehow needs to know these names when running genion.<br>
>><br>
>> My question is if there is a best choice for these names.<br>
>> Maybe some force fields have names for this?<br>
>> Is there a pdb or IUPAC standard (I guess this is capitalized without<br>
>> the sign)?<br>
>><br>
>> It would be convenient if all force fields use the same naming scheme.<br>
>><br>
>> Berk<br>
>><br>
>><br>
>><br>
><br>
><br>
<br>
--<br>
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</div></div></blockquote></div><br>