<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:10pt"><div>Hi Mark,<br><br>I tried but with this error:<br><br>Fatal error:<br>Number of atoms in pdb frame 0 is 331 instead of 491<br><br>Joyce<br></div><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mark Abraham &lt;Mark.Abraham@anu.edu.au&gt;<br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users &lt;gmx-users@gromacs.org&gt;<br><b><span style="font-weight: bold;">Sent:</span></b> Saturday, February 12, 2011 0:01:39<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] doubts on g_confrms output<br></font><br>

  
    
  
    On 12/02/2011 2:55 AM, Kwee Hong wrote:
    <blockquote type="cite">
      
      <div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">
        <div>Hi Tsjerk,<br>
          <br>
          Thanks for the help. I got it.<br>
          But do you have any idea how to solve this in vmd?<br>
        </div>
      </div>
    </blockquote>
    <br>
    Use trjconv -sep on the .pdb file to split it.<br>
    <br>
    Mark<br>
    <br>
    <blockquote type="cite">
      <div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">
        <div><br>
          Regards,<br>
          Joyce<br>
        </div>
        <div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><br>
          <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2">
              <hr size="1"><b><span style="font-weight: bold;">From:</span></b>
              Tsjerk Wassenaar <a rel="nofollow" class="moz-txt-link-rfc2396E" ymailto="mailto:tsjerkw@gmail.com" target="_blank" href="mailto:tsjerkw@gmail.com">&lt;tsjerkw@gmail.com&gt;</a><br>
              <b><span style="font-weight: bold;">To:</span></b>
              Discussion list for GROMACS users
              <a rel="nofollow" class="moz-txt-link-rfc2396E" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">&lt;gmx-users@gromacs.org&gt;</a><br>
              <b><span style="font-weight: bold;">Sent:</span></b>
              Saturday, January 22, 2011 15:53:22<br>
              <b><span style="font-weight: bold;">Subject:</span></b>
              Re: [gmx-users] doubts on g_confrms output<br>
            </font><br>
            <p>Hi Joyce,</p>
            <p>In pymol use 'set all_states'</p>
            <p>Cheers,</p>
            <p>Tsjerk</p>
            <blockquote type="cite">On Jan 22, 2011 8:30 AM, "Kwee Hong"
              &lt;<a rel="nofollow" ymailto="mailto:jestan1985@yahoo.com" target="_blank" href="mailto:jestan1985@yahoo.com">jestan1985@yahoo.com</a>&gt;
              wrote:<br>
              <br>
              <div>
                <div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">
                  <div>Hi,</div>
                  <div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">
                    <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">
                      <div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">
                        <div style="font-family: arial,helvetica,sans-serif; font-size: 10pt; color: rgb(0, 0, 0);">
                          <div><br>
                          </div>
                          <div>I was trying to do some analysis
                            following John's "GROMACS tutorial for
                            solvation study of spider toxin peptide".</div>
                          <div>I'm using GROMACS-4.5.3 and my command
                            line for g_confrms is&nbsp;</div>
                          <div><br>
                          </div>
                          <div>g_confrms -f1 1OMB.pdb -f2 md.gro -o
                            fit_wet.pdb</div>
                          <div><br>
                          </div>
                          <div>The program calculated the RMSD
                            sucessfully and fit_wet.pdb was generated.
                            Yet, when i tried to visualise fit_wet.pdb
                            using VMD, the structure is obviously in a
                            mess. And when I tried it out with pymol, I
                            can only visualised one model. Model 2 did
                            not appear. I wonder would it be the pdb
                            format generated by g_confrms is not the
                            standard pdb format and had caused VMD and
                            final failed to read them?</div>
                          <div><br>
                          </div>
                          <div>Herein, I attached part of the pdb file
                            generated by fit_wet.pdb. Any insight is
                            welcomed.</div>
                          <div><br>
                          </div>
                          <div>Thanks,</div>
                          <div>Joyce</div>
                        </div>
                      </div>
                      <br>
                    </div>
                  </div>
                </div>
                <br>
              </div>
              <br>
              --<br>
              gmx-users mailing list &nbsp; &nbsp;<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
              <a rel="nofollow" target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
              Please search the archive at <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">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 rel="nofollow" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
              Can't post? Read <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br>
            </blockquote>
          </div>
        </div>
      </div>
      <br>
    </blockquote>
    <br>
  </div></div>
</div><br></body></html>