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 <[email protected]> > Para: Discussion list for GROMACS users <[email protected]> > 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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
