the gro file was the input. I am attaching a pdb as well<div><br></div><div><div>CRYST1    100.0    100.0    100.0  90.00  90.00  90.00 P 1           1  </div><div>ATOM      1  P   G   A   4       5.488  -0.842   0.708  1.00  0.00           P</div>
<div>ATOM      2  OP1 G   A   4       6.418   0.258   1.047  1.00  0.00           O</div><div>ATOM      3  OP2 G   A   4       5.367  -1.998   1.624  1.00  0.00           O</div><div>ATOM      4  O5&#39; G   A   4       4.010  -0.213   0.513  1.00  0.00           O</div>
<div>ATOM      5  C5&#39; G   A   4       3.816   1.098   0.014  1.00  0.00           C</div><div>ATOM      6  C4&#39; G   A   4       2.324   1.432  -0.121  1.00  0.00           C</div><div>ATOM      7  O4&#39; G   A   4       1.623   0.448  -0.862  1.00  0.00           O</div>
<div>ATOM      8  C3&#39; G   A   4       1.584   1.482   1.211  1.00  0.00           C</div><div>ATOM      9  O3&#39; G   A   4       1.869   2.669   1.934  1.00  0.00           O</div><div>ATOM     10  C2&#39; G   A   4       0.136   1.413   0.721  1.00  0.00           C</div>
<div>ATOM     11  O2&#39; G   A   4      -0.363   2.696   0.397  1.00  0.00           O</div><div>ATOM     12  C1&#39; G   A   4       0.241   0.597  -0.574  1.00  0.00           C</div><div>ATOM     13  N9  G   A   4      -0.450  -0.705  -0.438  1.00  0.00           N</div>
<div>ATOM     14  C8  G   A   4       0.075  -1.954  -0.237  1.00  0.00           C</div><div>ATOM     15  N7  G   A   4      -0.808  -2.911  -0.197  1.00  0.00           N</div><div>ATOM     16  C5  G   A   4      -2.017  -2.251  -0.377  1.00  0.00           C</div>
<div>ATOM     17  C6  G   A   4      -3.346  -2.767  -0.450  1.00  0.00           C</div><div>ATOM     18  O6  G   A   4      -3.705  -3.941  -0.398  1.00  0.00           O</div><div>ATOM     19  N1  G   A   4      -4.299  -1.762  -0.593  1.00  0.00           N</div>
<div>ATOM     20  C2  G   A   4      -4.002  -0.413  -0.682  1.00  0.00           C</div><div>ATOM     21  N2  G   A   4      -5.023   0.438  -0.804  1.00  0.00           N</div><div>ATOM     22  N3  G   A   4      -2.751   0.071  -0.652  1.00  0.00           N</div>
<div>ATOM     23  C4  G   A   4      -1.809  -0.897  -0.499  1.00  0.00           C</div><div>ATOM     24  H5&#39; G   A   4       4.293   1.204  -0.960  1.00  0.00           H</div><div>ATOM     25 H5&#39;&#39; G   A   4       4.269   1.819   0.696  1.00  0.00           H</div>
<div>ATOM     26  H4&#39; G   A   4       2.217   2.395  -0.623  1.00  0.00           H</div><div>ATOM     27  H3&#39; G   A   4       1.819   0.589   1.792  1.00  0.00           H</div><div>ATOM     28  H2&#39; G   A   4      -0.503   0.940   1.465  1.00  0.00           H</div>
<div>ATOM     29 HO2&#39; G   A   4      -1.301   2.614   0.210  1.00  0.00           H</div><div>ATOM     30  H1&#39; G   A   4      -0.225   1.145  -1.393  1.00  0.00           H</div><div>ATOM     31  H8  G   A   4       1.129  -2.132  -0.139  1.00  0.00           H</div>
<div>ATOM     32  H1  G   A   4      -5.265  -2.065  -0.635  1.00  0.00           H</div><div>ATOM     33  H21 G   A   4      -5.974   0.099  -0.815  1.00  0.00           H</div><div>ATOM     34  H22 G   A   4      -4.841   1.428  -0.876  1.00  0.00           H</div>
<div>END</div><div><br></div><br><div class="gmail_quote">On Tue, Mar 22, 2011 at 2:43 PM, Daniel Adriano Silva M <span dir="ltr">&lt;<a href="mailto:dadriano@gmail.com">dadriano@gmail.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi,<div><br></div><div>Is this your input? (a GRO file?). Can you paste the PDB corresponding to the RNA nucleotide that you are interested on? I think the file may be small enough to paste it here so someone can try to reproduce what is happening to you.</div>

<div><br></div><div><font color="#888888">Daniel</font><div><div></div><div class="h5"><br><br><div class="gmail_quote">2011/3/22 maria goranovic <span dir="ltr">&lt;<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>&gt;</span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Sorry for the incomplete reply. <div>version 4.5.3, </div><div>command: pdb2gmx -f guan.pdb -ignh<div>I tried using -ter, but that did not help.</div><div><br></div><div><br></div><div>input coordinate file, pulled out from an RNA molecule. </div>


<div><br></div><div><div>Gromacs Runs On Most of All Computer Systems</div><div>   34</div><div>    1G        P    1   5.549   4.916   5.071</div><div>    1G      OP1    2   5.642   5.026   5.105</div><div>    1G      OP2    3   5.537   4.800   5.162</div>


<div>    1G      O5&#39;    4   5.401   4.979   5.051</div><div>    1G      C5&#39;    5   5.382   5.110   5.001</div><div>    1G      C4&#39;    6   5.232   5.143   4.988</div><div>    1G      O4&#39;    7   5.162   5.045   4.914</div>


<div>    1G      C3&#39;    8   5.158   5.148   5.121</div><div>    1G      O3&#39;    9   5.187   5.267   5.193</div><div>    1G      C2&#39;   10   5.014   5.141   5.072</div><div>    1G      O2&#39;   11   4.964   5.270   5.040</div>


<div>    1G      C1&#39;   12   5.024   5.060   4.943</div><div>    1G       N9   13   4.955   4.930   4.956</div><div>    1G       C8   14   5.008   4.805   4.976</div><div>    1G       N7   15   4.919   4.709   4.980</div>


<div>    1G       C5   16   4.798   4.775   4.962</div><div>    1G       C6   17   4.665   4.723   4.955</div><div>    1G       O6   18   4.630   4.606   4.960</div><div>    1G       N1   19   4.570   4.824   4.941</div>

<div>
    1G       C2   20   4.600   4.959   4.932</div><div>    1G       N2   21   4.498   5.044   4.920</div><div>    1G       N3   22   4.725   5.007   4.935</div><div>    1G       C4   23   4.819   4.910   4.950</div><div>

    1G      H5&#39;   24   5.429   5.120   4.904</div>
<div>    1G     H5&#39;&#39;   25   5.427   5.182   5.070</div><div>    1G      H4&#39;   26   5.222   5.240   4.938</div><div>    1G      H3&#39;   27   5.182   5.059   5.179</div><div>    1G      H2&#39;   28   4.950   5.094   5.146</div>


<div>    1G     HO2&#39;   29   4.870   5.261   5.021</div><div>    1G      H1&#39;   30   4.978   5.115   4.861</div><div>    1G       H8   31   5.113   4.787   4.986</div><div>    1G       H1   32   4.474   4.794   4.936</div>


<div>    1G      H21   33   4.403   5.010   4.918</div><div>    1G      H22   34   4.516   5.143   4.912</div><div>  10.00000  10.00000  10.00000</div><div><div></div><div><div><br></div><br><div class="gmail_quote">
On Tue, Mar 22, 2011 at 2:09 PM, 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

  
    
  
  <div text="#000000" bgcolor="#ffffff"><div>
    On 22/03/2011 8:15 PM, maria goranovic wrote:
    <blockquote type="cite">is this a bug of some kind then? someone ? anyone? <br>
    </blockquote>
    <br></div>
    It&#39;s still hard to say. I asked you for your GROMACS version and
    input coordinate file, and you didn&#39;t give us either (in full).
    While you&#39;re there, what pdb2gmx command did you use?<br><font color="#888888">
    <br>
    Mark</font><div><div></div><div><br>
    <br>
    <blockquote 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 href="mailto:mariagoranovic@gmail.com" target="_blank">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. 
            <div><br>
            </div>
            <div>
              <div>CRYST1    0.000    0.000    0.000  90.00  90.00
                 90.00 P 1           1</div>
              <div>ATOM      1  P   G   A   4       5.488  -0.842  
                0.708  1.00  0.00           P</div>
              <div>ATOM      2  OP1 G   A   4       6.418   0.258  
                1.047  1.00  0.00           O</div>
              <div>ATOM      3  OP2 G   A   4       5.367  -1.998  
                1.624  1.00  0.00           O</div>
              <div>ATOM      4  O5&#39; G   A   4       4.010  -0.213  
                0.513  1.00  0.00           O</div>
              <div>ATOM      5  C5&#39; G   A   4       3.816   1.098  
                0.014  1.00  0.00           C</div>
              <div>ATOM      6  C4&#39; G   A   4       2.324   1.432
                 -0.121  1.00  0.00           C</div>
              <div>ATOM      7  O4&#39; G   A   4       1.623   0.448
                 -0.862  1.00  0.00           O</div>
              <div>ATOM      8  C3&#39; G   A   4       1.584   1.482  
                1.211  1.00  0.00           C</div>
              <div>....</div>
              <div>ATOM     33  H21 G   A   4      -5.974   0.099
                 -0.815  1.00  0.00           H</div>
              <div>ATOM     34  H22 G   A   4      -4.841   1.428
                 -0.876  1.00  0.00           H</div>
              <div><br>
              </div>
              <div><br>
              </div>
              <div>
                <div>
                  <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>On Sat, Mar 19, 2011 at 5:44 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>
                </div>
                <blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
                  <div>
                    <div><br>
                      <br>
                      <span>On 19/03/11, <b>maria goranovic </b> &lt;<a 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&#39; 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? </div>
                        </div>
                      </blockquote>
                      <br>
                    </div>
                    That does sound suspicious, but it&#39;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? </div>
                        </div>
                      </blockquote>
                      <br>
                    </div>
                    The procedure is outlined here: <a 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    <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>
              <div><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>
  </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><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>


Copenhagen<br>
</div></div></div></div>
<br>--<br>
gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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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></div></div></div>
<br>--<br>
gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org">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">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><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>
Copenhagen<br>
</div>