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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"><<a moz-do-not-send="true"
href="mailto:mariagoranovic@gmail.com">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 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"><<a moz-do-not-send="true"
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 class="im">
<div><br>
<br>
<span>On 19/03/11, <b>maria goranovic </b> <<a
moz-do-not-send="true"
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
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>
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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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