That may seem ridiculous, but I&#39;m also using a *.gro file and whenever GROMACS tells me: &quot;File input/output error:&quot;, it means that I&#39;ve not cd to the folder in which that *.gro file exists!<br><br><br><div class="gmail_quote">
On Mon, Jul 13, 2009 at 6:59 AM, Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
mohit kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
ok.thanx very much .......so but it happens generally to all tutorials i have done..means...grompp not able to find .gro files....i have tried 3-4 tutorial..and i stuck at same place everytime. please tell me how to download coordinate files...<br>

</blockquote>
<br></div>
Use sftp.<br><font color="#888888">
<br>
-Justin<br>
<br>
</font><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
thnx again..for your help!!<br>
<br></div><div class="im">
On Sun, Jul 12, 2009 at 9:01 PM, Justin A. Lemkul &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt; wrote:<br>

<br>
<br>
<br>
    mohit kumar wrote:<br>
<br>
        i write down all steps till i got stuck...my server is using<br>
        4.0.2 version..ya fws_b4pr.gro is successfully created..someone<br>
        suggest me its may be due to excessive charge...i dnt get that<br>
        point.<br>
<br>
<br>
    I don&#39;t understand what &quot;excessive charge&quot; would be about.  All the<br>
    commands work perfectly on my local machine, therefore, they should<br>
    work.  I would be willing to bet that you&#39;re seeing a filesystem<br>
    blip and grompp can&#39;t find your coordinate file (either momentarily<br>
    or ever).  Again, I recommend downloading the coordinate file and<br>
    processing with grompp on a local machine.<br>
<br>
    -Justin<br>
<br>
        On Sun, Jul 12, 2009 at 8:16 PM, Justin A. Lemkul<br>
        &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br></div><div><div></div><div class="h5">
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt; wrote:<br>
<br>
<br>
<br>
           mohit kumar wrote:<br>
<br>
               oh!!!!..no i mean that instead of.pdb file i used .gro<br>
               file..from the begining...in the tutorial they dont change to<br>
               .gro type.. but i do...and i carefully apply....i am able<br>
        to run<br>
               mdrun command for energy minimisation..and in this command i<br>
               want output file ..so i used *-c fws_b4pr.gro*...but when<br>
        i ran<br>
               grompp for position restrained it show the error..though the<br>
               file has been created in directory/server<br>
<br>
<br>
           So fws_b4pr.gro was successfully created, but then grompp<br>
        can&#39;t find<br>
           it?  Maybe you&#39;re seeing some sort of network/NFS problem when<br>
           accessing the server.  Do you have a local machine where you<br>
        can try<br>
           again?  Otherwise, post all your commands exactly as you have<br>
           entered them to see if anyone can spot a typo or other problem.<br>
<br>
           -Justin<br>
<br>
               On Sun, Jul 12, 2009 at 7:47 PM, Justin A. Lemkul<br>
               &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;<br>
               &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt;&gt; wrote:<br>
<br>
<br>
<br>
                  mohit kumar wrote:<br>
<br>
                      im trying this spider toxin tutorial as beginner<br>
        ....the<br>
               mdrun<br>
                      command after energy minimization have *-c<br>
        fws_b4pr.pdb(i<br>
               make<br>
                      .gro)* and then on page  no 9 the grompp command<br>
        for the<br>
               postion<br>
                      restrained uses *-c fws_b4pr.gro* and when i run<br>
        it show:<br>
                      Program grompp, VERSION 4.0.2<br>
                      Source code file: futil.c, line: 330<br>
<br>
                      File input/output error:<br>
                      fws_b4pr.gro<br>
                      ------------------------------<br>
                      -------------------------<br>
<br>
                      &quot;Hey Man You Know, I&#39;m Really OK&quot; (Offspring)<br>
                      what may be the reason for this..im really confused!!!<br>
<br>
<br>
                  Probably a typo or you lack read/write permissions in the<br>
               directory.<br>
                   Otherwise, how did you &quot;make .gro?&quot;  Did you use<br>
        editconf,<br>
               or did<br>
                  you just rename the file?<br>
<br>
                  -Justin<br>
<br>
<br>
                      --        MOHIT KUMAR<br>
                      Molecular Biochemistry &amp; Biophysics<br>
                      Graduate Student<br>
                      Illinois Institute of Technology<br>
                      Chicago,IL, USA<br>
<br>
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                  --    ========================================<br>
<br>
                  Justin A. Lemkul<br>
                  Ph.D. Candidate<br>
                  ICTAS Doctoral Scholar<br>
                  Department of Biochemistry<br>
                  Virginia Tech<br>
                  Blacksburg, VA<br>
                  jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt;<br>
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               231-9080<br>
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                  <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<br>
<br>
<br>
               --        MOHIT KUMAR<br>
               Molecular Biochemistry &amp; Biophysics<br>
               Graduate Student<br>
               Illinois Institute of Technology<br>
               Chicago,IL, USA<br>
<br>
<br>
           --    ========================================<br>
<br>
           Justin A. Lemkul<br>
           Ph.D. Candidate<br>
           ICTAS Doctoral Scholar<br>
           Department of Biochemistry<br>
           Virginia Tech<br>
           Blacksburg, VA<br>
           jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (540)<br>
        231-9080<br>
           <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<br>
<br>
        --         MOHIT KUMAR<br>
        Molecular Biochemistry &amp; Biophysics<br>
        Graduate Student<br>
        Illinois Institute of Technology<br>
        Chicago,IL, USA<br>
<br>
<br>
    --     ========================================<br>
<br>
    Justin A. Lemkul<br>
    Ph.D. Candidate<br>
    ICTAS Doctoral Scholar<br>
    Department of Biochemistry<br>
    Virginia Tech<br>
    Blacksburg, VA<br>
    jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (540) 231-9080<br>
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<br>
-- <br>
MOHIT KUMAR<br>
Molecular Biochemistry &amp; Biophysics<br>
Graduate Student<br>
Illinois Institute of Technology<br>
Chicago,IL, USA<br>
<br>
</div></div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Negar Ashari Astani<br><br>