<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>That actually worked.</span></div><div><br><span></span></div><div><span>Thanks!<br></span></div><div><br></div> <div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">De:</span></b> Peter C. Lai <pcl@uab.edu><br> <b><span style="font-weight: bold;">Para:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Enviadas:</span></b> Sexta-feira, 30 de Março de 2012 21:08<br> <b><span style="font-weight: bold;">Assunto:</span></b> Re: [gmx-users] index.ndx files<br> </font> </div> <br>You do not need to use an index file if you aren't defining anything beyond<br>the
standard index groups. In that case do not use -n in grompp.<br><br>On 2012-03-30 05:06:34PM -0700, Eduardo Oliveira wrote:<br>> Thanks for the quick reply!<br>> <br>> Well, i tried to address the index file "indes.ndx" but as you already told <br>> me the file doesn't exist in the working directory. I actually don't <br>> have any idea how to solve this. Let me post all the routines i did so <br>> far so you can have a better idea of my problem.<br>> <br>> I sarted with:<br>> <br>> pdb2gmx_d -f arath.pdb -o sistema.pdb -p sistema.top (bold text are tmy files)<br>> <br>> <br>> Wich gave me the following files:<br>> - posre.itp<br>> - sistema.gro<br>> - sistema.top<br>> <br>> Then:<br>> <br>> editconf_d -bt dodecahedron -princ -f sistema.gro -o sistema_box.gro -c -d 1.0<br>> <br>> Then: <br>> <br>> <br>> genbox_d -cp sistema_box.gro -cs spc216.bro -o sistema_boxwater.gro -p
sistema.top<br>> <br>> 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 <br>> file artificially inside the working directory?<br>> <br>> <br>> <br>> <br>> <br>> ________________________________<br>> De: Mark Abraham <<a ymailto="mailto:Mark.Abraham@anu.edu.au" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>> Para: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>> <br>> Enviadas: Sexta-feira, 30 de Março de 2012 20:42<br>> Assunto: Re: [gmx-users] index.ndx files<br>> <br>> <br>> On 31/03/2012 10:39 AM, Eduardo Oliveira wrote: <br>> Hi,<br>> ><br>> ><br>> >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:<br>> ><br>> ><br>> >grompp_d -f stpr.mdp -c sistema_boxwater.gro -p sistema.top -o sistema_stpr.tpr -n <br>> ><br>> >Text in bold correspond to my files.<br>> ><br>> ><br>> ><br>> >This is what i got:<br>> ><br>> ><br>> >File input/output error:<br>> >index.ndx<br>> ><br>> If you specify -n, then grompp needs to be able to find and read a<br>> file. The default filename is index.ndx, but that isn't working. You<br>> need to find out why.<br>> <br>> Mark<br>> <br>> -- <br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at
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target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br><br>-- <br>==================================================================<br>Peter C. Lai | University of Alabama-Birmingham<br>Programmer/Analyst | KAUL 752A<br>Genetics, Div. of Research | 705 South 20th Street<br><a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL
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