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' G A 4 4.010 -0.213 0.513 1.00 0.00 O</div>
<div>ATOM 5 C5' G A 4 3.816 1.098 0.014 1.00 0.00 C</div><div>ATOM 6 C4' G A 4 2.324 1.432 -0.121 1.00 0.00 C</div><div>ATOM 7 O4' G A 4 1.623 0.448 -0.862 1.00 0.00 O</div>
<div>ATOM 8 C3' G A 4 1.584 1.482 1.211 1.00 0.00 C</div><div>ATOM 9 O3' G A 4 1.869 2.669 1.934 1.00 0.00 O</div><div>ATOM 10 C2' G A 4 0.136 1.413 0.721 1.00 0.00 C</div>
<div>ATOM 11 O2' G A 4 -0.363 2.696 0.397 1.00 0.00 O</div><div>ATOM 12 C1' 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' G A 4 4.293 1.204 -0.960 1.00 0.00 H</div><div>ATOM 25 H5'' G A 4 4.269 1.819 0.696 1.00 0.00 H</div>
<div>ATOM 26 H4' G A 4 2.217 2.395 -0.623 1.00 0.00 H</div><div>ATOM 27 H3' G A 4 1.819 0.589 1.792 1.00 0.00 H</div><div>ATOM 28 H2' G A 4 -0.503 0.940 1.465 1.00 0.00 H</div>
<div>ATOM 29 HO2' G A 4 -1.301 2.614 0.210 1.00 0.00 H</div><div>ATOM 30 H1' 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"><<a href="mailto:dadriano@gmail.com">dadriano@gmail.com</a>></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"><<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>></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' 4 5.401 4.979 5.051</div><div> 1G C5' 5 5.382 5.110 5.001</div><div> 1G C4' 6 5.232 5.143 4.988</div><div> 1G O4' 7 5.162 5.045 4.914</div>
<div> 1G C3' 8 5.158 5.148 5.121</div><div> 1G O3' 9 5.187 5.267 5.193</div><div> 1G C2' 10 5.014 5.141 5.072</div><div> 1G O2' 11 4.964 5.270 5.040</div>
<div> 1G C1' 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' 24 5.429 5.120 4.904</div>
<div> 1G H5'' 25 5.427 5.182 5.070</div><div> 1G H4' 26 5.222 5.240 4.938</div><div> 1G H3' 27 5.182 5.059 5.179</div><div> 1G H2' 28 4.950 5.094 5.146</div>
<div> 1G HO2' 29 4.870 5.261 5.021</div><div> 1G H1' 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"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></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'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><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"><<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>></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' G A 4 4.010 -0.213
0.513 1.00 0.00 O</div>
<div>ATOM 5 C5' G A 4 3.816 1.098
0.014 1.00 0.00 C</div>
<div>ATOM 6 C4' G A 4 2.324 1.432
-0.121 1.00 0.00 C</div>
<div>ATOM 7 O4' G A 4 1.623 0.448
-0.862 1.00 0.00 O</div>
<div>ATOM 8 C3' 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"><<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>></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> <<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>>
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? </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? </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>
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Technical University of Denmark<br>
Copenhagen<br>
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