[gmx-users] index.ndx files

[Peter C. Lai]

You do not need to use an index file if you aren't defining anything beyond
the standard index groups. In that case do not use -n in grompp.

On 2012-03-30 05:06:34PM -0700, Eduardo Oliveira wrote:
> Thanks for the quick reply!
> 
> Well, i tried to address the index file "indes.ndx" but as you already told 
> me the file doesn't exist in the working directory. I actually don't 
> have any idea how to solve this. Let me post all the routines i did so 
> far so you can have a better idea of my problem.
> 
> I sarted with:
> 
> pdb2gmx_d -f arath.pdb -o sistema.pdb -p sistema.top (bold text are tmy files)
> 
> 
> Wich gave me the following files:
> - posre.itp
> - sistema.gro
> - sistema.top
> 
> Then:
> 
> editconf_d -bt dodecahedron -princ -f sistema.gro -o sistema_box.gro -c -d 1.0
> 
> Then: 
> 
> 
> genbox_d -cp sistema_box.gro -cs spc216.bro -o sistema_boxwater.gro -p sistema.top
> 
> And the after that i used grompp_d wich returned me the input/output error. After that i keep failing miserably. Do i have to create an index.ndx 
> file artificially inside the working directory?
> 
> 
> 
> 
> 
> ________________________________
>  De: Mark Abraham <Mark.Abraham at anu.edu.au>
> Para: Discussion list for GROMACS users <gmx-users at gromacs.org> 
> Enviadas: Sexta-feira, 30 de Março de 2012 20:42
> Assunto: Re: [gmx-users] index.ndx files
>  
> 
> On 31/03/2012 10:39 AM, Eduardo Oliveira wrote: 
> Hi,
> >
> >
> >I'm trying to set up a configuration file to but i keep gettin an error after the grompp_d run. I'm using the command line as follows:
> >
> >
> >grompp_d -f stpr.mdp -c sistema_boxwater.gro -p sistema.top -o sistema_stpr.tpr -n 
> >
> >Text in bold correspond to my files.
> >
> >
> >
> >This is what i got:
> >
> >
> >File input/output error:
> >index.ndx
> >
> If you specify -n, then grompp needs to be able to find and read a
>     file. The default filename is index.ndx, but that isn't working. You
>     need to find out why.
> 
> Mark
> 
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Peter C. Lai			| University of Alabama-Birmingham
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