Hi Justin,<br> I have corrected the ffcharmm.itp file. But I am still getting the error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#<br>checking input for internal consistency...<br>processing topology...<br>Generated 0 of the 595 non-bonded parameter combinations<br>
<br>-------------------------------------------------------<br>Program grompp_d, VERSION 4.0.5<br>Source code file: toppush.c, line: 1273<br><br>Fatal error:<br>[ file topol.top, line 3879 ]:<br>Atom index (1) in settles out of bounds (1-0).<br>
This probably means that you have inserted topology section &quot;settles&quot;<br>in a part belonging to a different molecule than you intended to.<br>In that case move the &quot;settles&quot; section to the right molecule.<br>
-------------------------------------------------------<br><br>Thanks<br>Chanchal<br><br><br><div class="gmail_quote">On Tue, Aug 25, 2009 at 5:06 PM, 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>
Chanchal wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Justin,<br>
  Sorry, I attached the wrong file. Attached is the correct file.<br>
</blockquote>
<br></div>
There is a space after #define:<br>
<br>
#define _FF_CHARMM<br>
<br>
Your file has #define_FF_CHARMM.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks<br>
Chanchal<div class="im"><br>
<br>
<br>
On Tue, Aug 25, 2009 at 4:56 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>
    Chanchal wrote:<br>
<br></div><div><div></div><div class="h5">
        Hi Justin,<br>
         I am still getting the error message : Back Off! I just backed<br>
        up mdout.mdp to ./#mdout.mdp.2#<br>
        checking input for internal consistency...<br>
        processing topology...<br>
        Generated 0 of the 595 non-bonded parameter combinations<br>
<br>
        -------------------------------------------------------<br>
        Program grompp_d, VERSION 4.0.5<br>
        Source code file: toppush.c, line: 1273<br>
<br>
        Fatal error:<br>
        [ file topol.top, line 3879 ]:<br>
        Atom index (1) in settles out of bounds (1-0).<br>
        This probably means that you have inserted topology section<br>
        &quot;settles&quot;<br>
        in a part belonging to a different molecule than you intended to.<br>
        In that case move the &quot;settles&quot; section to the right molecule.<br>
        -------------------------------------------------------<br>
<br>
        As you said I added the line #define_FF_CHARMM in ffcharmm.itp.<br>
        Attached<br>
<br>
<br>
    The #define line is not present in that file.  Take care to use the<br>
    right files when you&#39;ve made changes.<br>
<br>
    -Justin<br>
<br>
        is the file.<br>
        Thanks<br>
        Chanchal<br>
<br>
<br>
        On Tue, Aug 25, 2009 at 4:42 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><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>
           Your ffcharmm.itp file lacks a necessary line at the very top:<br>
<br>
           #define _FF_CHARMM<br>
<br>
           Without this line, grompp does not know which force field you are<br>
           using, and hence everything breaks down when other .itp files are<br>
           called.<br>
<br>
           -Justin<br>
<br>
           Chanchal wrote:<br>
<br>
               Hi,<br>
                Attached are the top and itp file I am using. Please<br>
        help me to<br>
               fix the problem.<br>
               Thanks<br>
               Chanchal<br>
<br>
<br>
               On Tue, Aug 25, 2009 at 3:44 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>
                  Chanchal wrote:<br>
<br>
                      Hi All,<br>
                        I have downloaded pdb file and required .top and<br>
        .itp file<br>
                      from the site <a href="http://www.bioinf.uni-sb.de/RB/" target="_blank">http://www.bioinf.uni-sb.de/RB/</a> for DOPC<br>
                      simulation. Now when I execute the command<br>
                       grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p<br>
        topol.top -o<br>
                      dopc.tpr -e ener.edr -t traj.trr I got the error &quot;<br>
        Fatal<br>
               error:<br>
                      [ file tip3p.itp, line 42 ]:<br>
                      Atom index (1) in settles out of bounds (1-0).<br>
                      This probably means that you have inserted<br>
        topology section<br>
                      &quot;settles&quot;<br>
                      in a part belonging to a different molecule than you<br>
               intended to.<br>
                      In that case move the &quot;settles&quot; section to the right<br>
               molecule.<br>
                             -------------------------------------------------------<br>
<br>
                      Attached is the em.mdp file I am using. Please<br>
        help me how to<br>
                      solve this problem.<br>
<br>
<br>
                  Please see here:<br>
<br>
                               <a href="http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds" target="_blank">http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds</a><br>

<br>
                  The .mdp file is not the source of the problem; the<br>
        topology<br>
               is.  If<br>
                  you need more help, you&#39;ll have to post the relevant<br>
        section.<br>
<br>
                  -Justin<br>
<br>
                      Thanks<br>
                      Chanchal<br>
<br>
<br>
                                   ------------------------------------------------------------------------<br>
<br>
                      _______________________________________________<br>
                      gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;<br>
               &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;&gt;<br>
                      &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt; &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;&gt;&gt;<br>
<br>
<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<br>
        <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br>
                      before posting!<br>
                      Please don&#39;t post (un)subscribe requests to the<br>
        list. Use the<br>
                      www interface or send it to<br>
        <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a> &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;<br>

               &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;&gt;<br>
                      &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;<br>
               &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;&gt;&gt;.<br>
<br>
                      Can&#39;t post? Read<br>
               <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><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;<br>
        &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (540)<br>
<br>
               231-9080<br>
<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>
<br>
                  ========================================<br>
                  _______________________________________________<br>
                  gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;<br>
               &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;&gt;<br>
                  &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt; &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;&gt;&gt;<br>
<br>
<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<br>
        <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
                  posting!<br>
                  Please don&#39;t post (un)subscribe requests to the list.<br>
        Use the www<br>
                  interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;<br>
               &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;&gt;<br>
                  &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;<br>
               &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;&gt;&gt;.<br>
<br>
                  Can&#39;t post? Read<br>
        <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<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>
<br>
           ========================================<br>
           _______________________________________________<br>
           gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;<br>
           &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;&gt;<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 <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
           posting!<br>
           Please don&#39;t post (un)subscribe requests to the list. Use the www<br>
           interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;<br>
           &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
        &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;&gt;.<br>
           Can&#39;t post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<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>
    <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
    ========================================<br>
    _______________________________________________<br>
    gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
    &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;<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 <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
    posting!<br>
    Please don&#39;t post (un)subscribe requests to the list. Use the www<br>
    interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
    &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;.<br>
    Can&#39;t post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<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>
<br>
========================================<br>
_______________________________________________<br>
gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org" target="_blank">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 <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don&#39;t post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can&#39;t post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br>