[gmx-users] RE: Structure factor and g_rdf

[Luciano Costa]

Luciano Costa wrote:
> Hi Spoel,
>
>
> I have great admiration for your research and effort in the developement
> of gromacs. I have this how example and inspiration for my job. In the
> last week I wrote ask all lists about an question involving structure
> factor. I believe that the people in the list, in general,  it don't
> have pratice with structure factor. I have tried to use g_rdf program
> for to analyse trajectory file with respect structure factor. The system
> simulated is constituted by polymers. I have a program that to do
> (calculate) structure factor of xyz trajectory file. I did a program
> that convert *.trr file in *.xyz file, but I would like to obtain
> structure factor by g_rdf. Unfortunatelly, I had some problems with
> respect a " list (in the C source program) "  of atom type. Look this:
>
> Fatal error:
>
> Error: atom type (opls_557) not in list (18 types checked)!
>
> In the font program have:

This is a bug/missing feature in the sense that there are GROMOS atom
types hardcoded in the program. I will have a look, but it should be
quite easy to fix for yourself if you update t_cmTAble all the way up in
the file. If you look closely you'll see that all the H entries are
dientical etc. If you have other atom types then please try to find the
correspoonding scattering factors..


>
> #################################
> int return_atom_type (char *type)
> {
>   int i;
>
>   for (i = 0; (i < asize(CM_t)); i++)
>     if (!strcmp (type, CM_t[i].Label))
>       return i;
>   gmx_fatal(FARGS,"\nError: atom type (%s) not in list (%d types
> checked)!\n",
>               type,i);
>
>   return 0;
> }
> #################################
>
> I think that it search a string that correspond to atom type in
> opls_XXX. When I had construct my input  file and how the system wasn't
> protein or biomolecules, being polymers,  I setted new opls_XXX.
>
> Well, I don't know what to do now, because *.gro and topol.top files are
> ok. MD simulation is ok.
>
> Can you help me, please ?!
>
>
> Regards.
>
> very very thanks and, more time, congratulations by your effort and work.
>
>
>
>
>
>
> --
> ##     Luciano Tavares da Costa       ###
> Laboratory of Molecular Spectroscopy
> ## Zipe Code:05508-000 IQ-USP Brazil#
> ##################################


--
David.
________________________________________________________________________

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


--
##             Luciano Tavares da Costa                ###
---->    Laboratory of Molecular
Spectroscopy    <-----                                                
       #
http://lem.iq.usp.br; mailto: ltcnikit at gmail.com  #      ##          Zipe
Code:05508-000 IQ-USP Brazil       ##
###########################################
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