Hi again,<br>
I just found pdb files of sugars in <a href="http://www.nyu.edu/pages/mathmol/library/sugars/">http://www.nyu.edu/pages/mathmol/library/sugars/</a><br>
So I think the next step is to use
the genbox, right? With this should be possible to multiply my sugar
molecules and to put them in random positions. Well I am not sure about
this because I am new as Gromac user, so any consideration about would
be helpful for me.<br>
Thanks again,<br>
Fernando Mattio<br><br><div><span class="gmail_quote">2005/10/5, Fernando Mattio <<a href="mailto:mattiofer@gmail.com">mattiofer@gmail.com</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Tsjerk and Gromacs users,<br> Thank
you for your answer Tsjerk, but I am still a little bit confused. What
I would like to have is a protein in a box of water, with molecules of
sugar present in the system, I mean in random positions. So I think I
donīt need sugar chains... <br>
What I understood from your answer is that I need an .itp
file of sugar to be added in the topology file, is it right? The
problem is that I could not find in the Gromacs files an itp file for
sugar, only .rtp, so do I have to create it or is it already done
somewhere that I could not find? <br>
<br>
<table style="width: 323px;" border="1" cellpadding="1" cellspacing="0">
<tbody><tr><th colspan="6">Sugars</th>
</tr><tr><td>
<br>
</td></tr><tr><td>GALB </td><td>ffgmx.rtp</td><td> - </td><td>galactose-B</td><td>C<sub>6</sub>H<sub>10</sub>O<sub>5</sub></td><td>-
</td></tr><tr><td>GLCA </td><td>ffgmx.rtp</td><td> - </td><td>glucose-A</td><td>C<sub>6</sub>H<sub>10</sub>O<sub>5</sub></td><td>-
</td></tr><tr><td>GLCB </td><td>ffgmx.rtp</td><td> - </td><td>glucose-B</td><td>C<sub>6</sub>H<sub>10</sub>O<sub>5</sub></td><td>-</td></tr></tbody>
</table>
<br>
<br>
And then to "multiply" my molecules of sugar and to add
them to my system in random positions, what programs should I use?<span class="q"><br>
<br>
Thank you very much in advance,<br>
Fernando Mattio<br></span><div><span class="gmail_quote"><br>
<br>
<br>
2005/10/5, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">tsjerkw@gmail.com</a>>:</span><div><span class="e" id="q_106c10c4aa5d3ac2_3"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Fernando,<br>
<br>
Unless you're trying to build sugar chains, you don't need to make
building blocks in the .rtp file. It is better to use .itp files for
them. Also, it's better not to use the gmx force field, but rather the
GROMOS one, for which there should be good sugar parameters available
(by Roberto Lins).<br>
And genbox doesn't use the .rtp file, it's only used by pdb2gmx. Genbox will insert molecules from a structure file (gro, pdb).<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br>
<br>
<br><div><div><span><span class="gmail_quote">On 10/5/05, <b class="gmail_sendername">Fernando Mattio</b> <<a href="mailto:mattiofer@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
mattiofer@gmail.com</a>> wrote:</span></span></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><span>
Dear Gromacs users,<br>
<br>
I would like to insert some molecules of sugar in a box with protein
and water . So my idea was to use the ffgmx.rtp file, but copying
only the information of for example GALB and saving it as other
.rtp file. It is the first time that I am dealing with this kind of
topology file, and I would like to know if it is the right way of using
the Gromacs Building Blocks.<br>
Then with genbox I think it is possible to create other sugar molecules
from the .rtp file and to add them to my system, is it right?<br>
<br>
Thank you very much in advance!<br><span>
Fernando Mattio<br>
<br>
</span><br></span></div>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org
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gmx-users-request@gromacs.org</a>.<br><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry
<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>
</blockquote></span></div></div><br>
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