Hi,<br><br>First of all, sorry about my last email. <br><br>Berk, yes. My suggestion is issue 2).<br><br>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. <br>
<br>The function what I mentioned I wrote below:<br><br>type_ions_t get_ion_id(char * ion_name){<br><br> if (strcmp(ion_name,"CL-")==0) {<br> return ionCL_<br> }else if (strcmp(ion_name,"CL")==0) {<br>
return ionCL<br>}<br><br>enum type_ion {ionCL, ionCL_, ionNR}<br>typedef enum type_ion type_ion_t<br><br>Each force-field may has a structure to inform which ions id it works:<br><br>typedef struct sions_force_field{<br>
type_ion type_ion_t<br>}ions_force_field_t<br><br>ions_force_field_t ions_charmm [] = { {ionCL}, {ionCL_}};<br><br>I hope that I wrote more clear my idea. <br><br>Thanks in advance,<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 12:05 PM, Ran Friedman <span dir="ltr"><<a href="mailto:r.friedman@bioc.uzh.ch">r.friedman@bioc.uzh.ch</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000">
Hi,<br>
<br>
<div align="justify">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).<br>
<br>
Problems:<br>
(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.<br>
(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.<br>
</div>
<br>
Thanks,<br>
Ran<div><div></div><div class="h5"><br>
<br>
Berk Hess wrote:
<blockquote cite="http://mid4C504414.9050204@cbr.su.se" type="cite">
<pre>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:
</pre>
<blockquote type="cite">
<pre>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]
<a href="http://gitorious.org/protpred-gromacs/protpred-gromacs/blobs/master/include/enums.h" target="_blank">http://gitorious.org/protpred-gromacs/protpred-gromacs/blobs/master/include/enums.h</a>
--
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
<a href="http://laips.sel.eesc.usp.br" target="_blank">http://laips.sel.eesc.usp.br</a>
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218" target="_blank">http://lattes.cnpq.br/1025157978990218</a>
Public Profile - <a href="http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5" target="_blank">http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5</a>
On Wed, Jul 28, 2010 at 7:29 AM, Berk Hess <<a href="mailto:hess@cbr.su.se" target="_blank">hess@cbr.su.se</a>
<a href="mailto:hess@cbr.su.se" target="_blank"><mailto:hess@cbr.su.se></a>> 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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</pre>
</blockquote>
<pre> </pre>
</blockquote>
<br>
<br>
</div></div><pre cols="72">--
------------------------------------------------------
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: <a href="mailto:r.friedman@bioc.uzh.ch" target="_blank">r.friedman@bioc.uzh.ch</a>
Skype: ran.friedman
------------------------------------------------------
</pre>
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