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    On 22/03/2011 8:15 PM, maria goranovic wrote:
    <blockquote
      cite="mid:AANLkTimG5FOV1LxLWn+6EboamHDgYKDuE8JarCXYgiR4@mail.gmail.com"
      type="cite">is this a bug of some kind then? someone ? anyone? <br>
    </blockquote>
    <br>
    It's still hard to say. I asked you for your GROMACS version and
    input coordinate file, and you didn't give us either (in full).
    While you're there, what pdb2gmx command did you use?<br>
    <br>
    Mark<br>
    <br>
    <blockquote
      cite="mid:AANLkTimG5FOV1LxLWn+6EboamHDgYKDuE8JarCXYgiR4@mail.gmail.com"
      type="cite">
      <div>just bumping,</div>
      <div><br>
      </div>
      <div>maria<br>
        <br>
        <div class="gmail_quote">On Mon, Mar 21, 2011 at 10:17 AM, maria
          goranovic <span dir="ltr">&lt;<a moz-do-not-send="true"
              href="mailto:mariagoranovic@gmail.com">mariagoranovic@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;">Here are the contents of my input
            coordinate file.&nbsp;
            <div><br>
            </div>
            <div>
              <div>CRYST1 &nbsp; &nbsp;0.000 &nbsp; &nbsp;0.000 &nbsp; &nbsp;0.000 &nbsp;90.00 &nbsp;90.00
                &nbsp;90.00 P 1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 1</div>
              <div>ATOM &nbsp; &nbsp; &nbsp;1 &nbsp;P &nbsp; G &nbsp; A &nbsp; 4 &nbsp; &nbsp; &nbsp; 5.488 &nbsp;-0.842 &nbsp;
                0.708 &nbsp;1.00 &nbsp;0.00 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; P</div>
              <div>ATOM &nbsp; &nbsp; &nbsp;2 &nbsp;OP1 G &nbsp; A &nbsp; 4 &nbsp; &nbsp; &nbsp; 6.418 &nbsp; 0.258 &nbsp;
                1.047 &nbsp;1.00 &nbsp;0.00 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; O</div>
              <div>ATOM &nbsp; &nbsp; &nbsp;3 &nbsp;OP2 G &nbsp; A &nbsp; 4 &nbsp; &nbsp; &nbsp; 5.367 &nbsp;-1.998 &nbsp;
                1.624 &nbsp;1.00 &nbsp;0.00 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; O</div>
              <div>ATOM &nbsp; &nbsp; &nbsp;4 &nbsp;O5' G &nbsp; A &nbsp; 4 &nbsp; &nbsp; &nbsp; 4.010 &nbsp;-0.213 &nbsp;
                0.513 &nbsp;1.00 &nbsp;0.00 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; O</div>
              <div>ATOM &nbsp; &nbsp; &nbsp;5 &nbsp;C5' G &nbsp; A &nbsp; 4 &nbsp; &nbsp; &nbsp; 3.816 &nbsp; 1.098 &nbsp;
                0.014 &nbsp;1.00 &nbsp;0.00 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; C</div>
              <div>ATOM &nbsp; &nbsp; &nbsp;6 &nbsp;C4' G &nbsp; A &nbsp; 4 &nbsp; &nbsp; &nbsp; 2.324 &nbsp; 1.432
                &nbsp;-0.121 &nbsp;1.00 &nbsp;0.00 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; C</div>
              <div>ATOM &nbsp; &nbsp; &nbsp;7 &nbsp;O4' G &nbsp; A &nbsp; 4 &nbsp; &nbsp; &nbsp; 1.623 &nbsp; 0.448
                &nbsp;-0.862 &nbsp;1.00 &nbsp;0.00 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; O</div>
              <div>ATOM &nbsp; &nbsp; &nbsp;8 &nbsp;C3' G &nbsp; A &nbsp; 4 &nbsp; &nbsp; &nbsp; 1.584 &nbsp; 1.482 &nbsp;
                1.211 &nbsp;1.00 &nbsp;0.00 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; C</div>
              <div>....</div>
              <div>ATOM &nbsp; &nbsp; 33 &nbsp;H21 G &nbsp; A &nbsp; 4 &nbsp; &nbsp; &nbsp;-5.974 &nbsp; 0.099
                &nbsp;-0.815 &nbsp;1.00 &nbsp;0.00 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; H</div>
              <div>ATOM &nbsp; &nbsp; 34 &nbsp;H22 G &nbsp; A &nbsp; 4 &nbsp; &nbsp; &nbsp;-4.841 &nbsp; 1.428
                &nbsp;-0.876 &nbsp;1.00 &nbsp;0.00 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; H</div>
              <div><br>
              </div>
              <div><br>
              </div>
              <div>
                <div class="im">
                  <div>
                    <blockquote type="cite" style="border-left: 1px
                      solid rgb(0, 0, 255); padding-left: 13px;
                      margin-left: 0pt;">
                      <div>
                        <div>Of course it would be best if pdb2gmx
                          worked as it is if I just have a single
                          nucleotide, and not a chain?</div>
                      </div>
                    </blockquote>
                    <br>
                  </div>
                </div>
                Here, I am wondering if the above problem is occurring
                because pdb2gmx is not being able to deal with an
                isolated nucleotide (while it might be able to deal with
                an polymer)</div>
              <div><br>
              </div>
              <div>Maria</div>
              <div><br>
              </div>
              <br>
              <div class="gmail_quote">
                <div class="im">On Sat, Mar 19, 2011 at 5:44 AM, Mark
                  Abraham <span dir="ltr">&lt;<a moz-do-not-send="true"
                      href="mailto:mark.abraham@anu.edu.au"
                      target="_blank">mark.abraham@anu.edu.au</a>&gt;</span>
                  wrote:<br>
                </div>
                <blockquote class="gmail_quote" style="margin: 0pt 0pt
                  0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
                  padding-left: 1ex;">
                  <div class="im">
                    <div><br>
                      <br>
                      <span>On 19/03/11, <b>maria goranovic </b> &lt;<a
                          moz-do-not-send="true"
                          href="mailto:mariagoranovic@gmail.com"
                          target="_blank">mariagoranovic@gmail.com</a>&gt;
                        wrote:</span>
                      <blockquote style="border-left: 1px solid rgb(0,
                        0, 255); padding-left: 13px; margin-left: 0pt;"
                        type="cite">
                        <div>Dear All
                          <div><br>
                          </div>
                          <div>I am trying to generate a topology for
                            guanosine monophosphate: i.e. an RNA base
                            with a phosphate at the 5' Carbon. I tried
                            to read in a pdb file containing all atoms,
                            and used pdb2gmx with CHARMM. However, the
                            output coordinate file has no phosphate
                            group on it. Why does the phosphate
                            disappear, and why does pdb2gmx not even
                            give me a warning?&nbsp;</div>
                        </div>
                      </blockquote>
                      <br>
                    </div>
                    That does sound suspicious, but it's hard to say
                    what went wrong. What GROMACS version was it, and
                    what were the contents of your input coordinate
                    file?
                    <div><br>
                      <br>
                      <blockquote style="border-left: 1px solid rgb(0,
                        0, 255); padding-left: 13px; margin-left: 0pt;"
                        type="cite">
                        <div>
                          <div>Assuming that a molecule like GMP does
                            not have a topology, I am guessing I might
                            have to make a new residue within CHARMM.
                            that should not be too much work because
                            there is no new angle/dihedral/bond/atom
                            type to be be added. Can someone please help
                            me with a simple workflow so I do not miss
                            something important?&nbsp;</div>
                        </div>
                      </blockquote>
                      <br>
                    </div>
                    The procedure is outlined here: <a
                      moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field"
                      target="_blank">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a>
                    Your case should be a reasonably straightforward
                    exercise in assigning sensible atom types from the
                    pre-existing options.
                    <div>
                      <br>
                      <br>
                      <blockquote style="border-left: 1px solid rgb(0,
                        0, 255); padding-left: 13px; margin-left: 0pt;"
                        type="cite">
                        <div>
                          <div><br>
                          </div>
                        </div>
                      </blockquote>
                    </div>
                  </div>
                  <font color="#888888"><br>
                    Mark
                  </font><br>
                  --<br>
                  gmx-users mailing list &nbsp; &nbsp;<a moz-do-not-send="true"
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                </blockquote>
              </div>
              <div class="im"><br>
                <br clear="all">
                <br>
                -- <br>
                Maria G.<br>
                Technical University of Denmark<br>
                Copenhagen<br>
              </div>
            </div>
          </blockquote>
        </div>
        <br>
        <br clear="all">
        <br>
        -- <br>
        Maria G.<br>
        Technical University of Denmark<br>
        Copenhagen<br>
      </div>
    </blockquote>
    <br>
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