[gmx-users] Re: structure factor

[Luciano Costa]

Hi Warren and gmx'users,

I tried what Warren ask me in the last e-mail and I still had some problems.
Look this --->

I read your answer about my ask 'structure factor' and I did what you wrote,
but the g_rdf searching a list and return the message:

##########
Fatal error:

Error: atom type (opls_557) not in list (18 types checked)!
#########

In the font program of gmx_rdf.c have:

#################################
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.

Why would be this list ?!?!? It would be a table with default atom type of
gromacs ?!?! What should I do in this case, because the MD simulations are
ok !!


thanks !!!!

------------------------------
>
> Message: 9
> Date: Thu, 06 Apr 2006 10:13:53 +1000
> From: "Dallas B. Warren" <Dallas.Warren at vcp.monash.edu.au>
> Subject: RE: [gmx-users] structural factor with g_rdf
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <89907EA1DCFB7548A431C13A270F9DD5017E9023 at prk-exch-01.vcp.local>
> Content-Type: text/plain; charset=US-ASCII
>
> I think you may find it is referring to a .tpr file.
>
> So use the -s switch, with the .tpr file that is associated with the
> trajectory file you are analysing.
>
> Catch ya,
>
> Dr. Dallas Warren
> Lecturer
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9524
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble
> a nail.
>
>
> ------------------------------
>
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>
>
> End of gmx-users Digest, Vol 24, Issue 16
> *****************************************
>



--
### Luciano Tavares da Costa ###
##       MSc. Eng. Químico
##       100 % Linux
#############################
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