<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Thanks for the quick reply!</span></div><div><br><span></span></div><div><span>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.</span></div><div><br><span></span></div><div><span>I sarted with:</span></div><div><br><span></span></div><div><span>pdb2gmx_d -f <span style="font-weight:bold;">arath.pdb</span> -o <span style="font-weight:bold;">sistema.pdb</span> -p <span style="font-weight:bold;">sistema.top </span><span>(bold text are tmy files)</span><span style="font-weight:bold;"><br></span></span></div><div><br><span></span></div><div><span>Wich gave me the following files:</span></div><div><span>-
posre.itp</span></div><div><span>- sistema.gro</span></div><div><span>- sistema.top</span></div><div><br><span></span></div><div><span>Then:</span></div><div><br><span></span></div><div><span>editconf_d -bt dodecahedron -princ -f sistema.gro -o sistema_box.gro -c -d 1.0</span></div><div><br><span></span></div><div><span>Then: <br></span></div><div><span><br></span></div><div><span>genbox_d -cp sistema_box.gro -cs spc216.bro -o sistema_boxwater.gro -p sistema.top</span></div><div><br><span></span></div><div><span>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?<br></span></div><div><span><br></span></div><div><br></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> Mark Abraham <Mark.Abraham@anu.edu.au><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 20:42<br> <b><span style="font-weight: bold;">Assunto:</span></b> Re: [gmx-users] index.ndx files<br> </font> </div> <br><div id="yiv253042688">
<div>
On 31/03/2012 10:39 AM, Eduardo Oliveira wrote:
<blockquote type="cite">
<div style="color:#000;background-color:#fff;font-family:arial, helvetica, sans-serif;font-size:12pt;">
<div>Hi,</div>
<div><br>
</div>
<div>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:</div>
<div><br>
</div>
<div>grompp_d -f <span style="font-weight:bold;">stpr.mdp</span>
-c <span style="font-weight:bold;">sistema_boxwater.gro</span>
-p <span style="font-weight:bold;">sistema.top</span> -o <span style="font-weight:bold;">sistema_stpr.tpr</span> -n <br>
</div>
<div><span style="background-color:rgb(255, 255, 0);">Text in
bold correspond to my files.</span><br>
</div>
<div><br>
</div>
<div>This is what i got:</div>
<div><br>
</div>
<div>File input/output error:<br>
index.ndx</div>
<br>
</div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
</div>
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