[gmx-users] index.ndx files

Eduardo Oliveira eduardobio at yahoo.com.br
Sat Mar 31 02:06:34 CEST 2012

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


editconf_d -bt dodecahedron -princ -f sistema.gro -o sistema_box.gro -c -d 1.0


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: 
>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:
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.


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