<p>Thanks Mark and Justin for your input. it works. For progeny, here&#39;s how:</p>
<p>1. In case of multiple, separate chains of protein, generate a <u>new</u> tpr X that does not include chain information. <br>
2. From X generate a new tpr file Y, consisting now only of the group under scrutiny (for example, backbone. Use tpbconv).<br>
3. Make new index file for Y.<br>
4. Now use trjconv to make xtc1  and xtc2 that consist only on that group. <br>
5. Use g_rms with Y tpr, the generate xtcs, and the new index group.</p>
<p>This should work and avoid the notorious segmentation fault (as long as you make sure the group you choose, backbone for example, has identical number of atoms in both xtc1 and xtc2).</p>
<p>-SA</p>
<div class="gmail_quote">On Tue, Sep 13, 2011 at 11:17 AM, Mark Abraham <span dir="ltr">&lt;<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">


  
    
  
  <div bgcolor="#FFFFFF" text="#000000"><div>
    On 13/09/2011 6:11 PM, Shay Teaching wrote:
    <blockquote type="cite">
      <div dir="ltr">Ok I tried that and it doesn&#39;t work:<br>
        There&#39;s a fundamental difference between chains/no-chains
        topology, namely the existence of peptide bond between chains,
        and the different protonation state on the termini.<br>
        In the chain-based topology there are several termini, and less
        peptide bonds.<br>
        <br>
        This causes the no-chains-tpr to have different number of atoms,
        and different protonation states.<br>
        I tried using tpbconv to make a backbone-tpr, but it still gets
        me to segmentation fault.<br>
      </div>
    </blockquote>
    <br></div>
    The idea behind Justin&#39;s original solution is still right. You need
    to provide two sets of corresponding atoms and those sets have to
    have the same size. So you need to construct two index groups that
    suit what you actually want to compare - say, the backbone atoms
    that are common to the two forms. That will require some thought,
    and playing around with make_ndx (or a text editor). Then use those
    to create subset .tpr and trajectory files as Justin suggested. Each
    form is likely to need its own customized index group to make the
    subset that is correct for it.<br><font color="#888888">
    <br>
    Mark</font><div><div></div><div><br>
    <br>
    <blockquote type="cite">
      <div dir="ltr">
        <br>
        So thanks, but I don&#39;t think it would work.<br>
        -SA<br>
        <br>
        <div class="gmail_quote">On Mon, Sep 12, 2011 at 11:47 PM, Shay
          Teaching <span dir="ltr">&lt;<a href="mailto:shay.teaching@gmail.com" target="_blank">shay.teaching@gmail.com</a>&gt;</span>
          wrote:<br>
          <blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
            <div dir="ltr">Thanks, I&#39;ll try that, and post again if it
              works.
              <div>
                <div>
                  <br>
                  <br>
                  <div class="gmail_quote">On Mon, Sep 12, 2011 at 6:20
                    PM, Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;</span>
                    wrote:<br>
                    <blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
                      <div><br>
                        <br>
                        Shay Teaching wrote:<br>
                        <blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
                          When I try to work the command on a small
                          portion of the backbone it seems to work just
                          fine. But when I try the entire backbone
                          (which is composed of several _separate_
                          chains) I am getting segmentation fault.<br>
                          Any workaround for that, so I can use the
                          entire backbone?<br>
                        </blockquote>
                        <br>
                      </div>
                      Are there chain identifiers separating the
                      proteins?  I don&#39;t know if that would cause the
                      problem, but it&#39;s possible.  In that case, I&#39;d
                      suggest you start with a coordinate file and
                      topology without chain identifiers and generate a
                      new .tpr file (and then take the backbone atoms
                      only with tpbconv).<br>
                      <br>
                      -Justin<br>
                      <br>
                      <blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
                        Thanks again,<br>
                        -Shay
                        <div>
                          <div><br>
                            <br>
                            On Mon, Sep 12, 2011 at 5:29 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>
                               Shay Teaching wrote:<br>
                            <br>
                                   Hi all,<br>
                                   (Gromacs 4.0.7): I am trying to make
                            rms matrix between one Wt<br>
                                   trajectory and one mutant trajectory
                            using the following command:<br>
                            <br>
                                   g_rms -f wt.xtc -f2 mutant.xtc -s
                            wt.tpr -m -fit rot+trans -n<br>
                                   wt_backbone.ndx<br>
                            <br>
                                   The file wt_backbone.ndx contains the
                            backbone of the protein<br>
                                   (Backbone indices are identical
                            between wt and mutant).<br>
                            <br>
                                   The result is that I am getting a
                            well deserved error saying<br>
                                   that wt.xtc and mutant.xtc has
                            different number of atoms (the<br>
                                   tpr itself):<br>
                                   Fatal error:<br>
                                   Second trajectory (76128 atoms) does
                            not match the first one<br>
                                   (76129 atoms)<br>
                            <br>
                                   So the question becomes: Is there a
                            (convenient) way to produce<br>
                                   rms-matrix between wt and mutant?<br>
                                   Or perhaps circumvent this problem in
                            some other way?<br>
                            <br>
                            <br>
                               Use trjconv to write out new trajectories
                            containing only backbone<br>
                               atoms of each protein, then use tpbconv
                            to write a .tpr file with<br>
                               only backbone atoms in it (using index
                            groups, if necessary).  Then<br>
                               run g_rms again with these new
                            trajectories and .tpr file.<br>
                                Everything should match if the indices
                            are chosen correctly.<br>
                            <br>
                               -Justin<br>
                            <br>
                               --     ==============================__==========<br>
                            <br>
                               Justin A. Lemkul<br>
                               Ph.D. Candidate<br>
                               ICTAS Doctoral Scholar<br>
                               MILES-IGERT Trainee<br>
                               Department of Biochemistry<br>
                               Virginia Tech<br>
                               Blacksburg, VA<br>
                          </div>
                        </div>
                           jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a><span style="padding-right:16px;width:16px;min-height:16px"></span> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a><span style="padding-right:16px;width:16px;min-height:16px"></span>&gt; | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540)
                          231-9080</a><br>
                           &lt;tel:%28540%29%20231-9080&gt;
                        <div><br>
                             <a href="http://www.bevanlab.biochem." target="_blank">http://www.bevanlab.biochem.</a><span style="padding-right:16px;width:16px;min-height:16px"></span>__<a href="http://vt.edu/Pages/Personal/justin" target="_blank">vt.edu/Pages/Personal/justin</a><span style="padding-right:16px;width:16px;min-height:16px"></span><br>


                             &lt;<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><span style="padding-right:16px;width:16px;min-height:16px"></span>&gt;<br>


                          <br>
                             ==============================__==========<br>
                             --     gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
                        </div>
                           &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;
                        <div><br>
                             <a href="http://lists.gromacs.org/__mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/__mailman/listinfo/gmx-users</a><span style="padding-right:16px;width:16px;min-height:16px"></span><br>


                             &lt;<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><span style="padding-right:16px;width:16px;min-height:16px"></span>&gt;<br>


                             Please search the archive at<br>
                             <a href="http://www.gromacs.org/__Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/__Support/Mailing_Lists/Search</a><span style="padding-right:16px;width:16px;min-height:16px"></span><br>


                             &lt;<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a><span style="padding-right:16px;width:16px;min-height:16px"></span>&gt; before
                          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>
                        </div>
                           &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;.
                        <div><br>
                             Can&#39;t post? Read <a href="http://www.gromacs.org/__Support/Mailing_Lists" target="_blank">http://www.gromacs.org/__Support/Mailing_Lists</a><span style="padding-right:16px;width:16px;min-height:16px"></span><br>


                        </div>
                        <div>    &lt;<a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><span style="padding-right:16px;width:16px;min-height:16px"></span>&gt;<br>


                          <br>
                          <br>
                        </div>
                      </blockquote>
                      <div>
                        <div>
                          <br>
                          -- <br>
                          ========================================<br>
                          <br>
                          Justin A. Lemkul<br>
                          Ph.D. Candidate<br>
                          ICTAS Doctoral Scholar<br>
                          MILES-IGERT Trainee<br>
                          Department of Biochemistry<br>
                          Virginia Tech<br>
                          Blacksburg, VA<br>
                          jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a><span style="padding-right:16px;width:16px;min-height:16px"></span> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540)
                            231-9080</a><br>
                          <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><span style="padding-right:16px;width:16px;min-height:16px"></span><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><span style="padding-right:16px;width:16px;min-height:16px"></span><br>


                          Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a><span style="padding-right:16px;width:16px;min-height:16px"></span> 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/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><span style="padding-right:16px;width:16px;min-height:16px"></span><br>


                        </div>
                      </div>
                    </blockquote>
                  </div>
                  <br>
                </div>
              </div>
            </div>
          </blockquote>
        </div>
        <br>
      </div>
      <br>
      <fieldset></fieldset>
      <br>
    </blockquote>
    <br>
  </div></div></div>

<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/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don&#39;t post (un)subscribe requests to the list. Use the<br>
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/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br>