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><span class="gmail_quote">On 10/5/05, <b class="gmail_sendername">Fernando Mattio</b> <<a href="mailto:mattiofer@gmail.com">mattiofer@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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 class="sg">
Fernando Mattio<br>
<br>
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<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>