Hi Peter,<br>
<br>
I know that the GROMOS building blocks also comprise the termini. You
should be able to add those to the terminal databases (.ntb and .ctb). <br>
Shouldn't take too much time if you understand the format. Unfortunately I have no time to spare now :(<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 5/15/06, <b class="gmail_sendername">Peter I. Hansen</b> <<a href="mailto:piha@kvl.dk">piha@kvl.dk</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;">
Hi<br><br>The 53a5 and 53a6 sets do have sugar residues, but it seems this is only<br>designed for 1->4 linkages, and does not provides atoms for start and<br>end groups. How do you propose to build a complete carbohydrate from this?
<br><br>thanks, Peter<br><br>Tsjerk Wassenaar wrote:<br>> Hi Peter,<br>><br>> You can define a building block in the .rtp file. For the parameters you<br>> should check out the GROMOS 43a5 force field (notably a paper by Roberto
<br>> Lins). Sugar parameters are also available in the 53a5 and 53a6 force<br>> field sets, which I thought were on the contributions page.<br>><br>> Cheers,<br>><br>> Tsjerk<br>><br>> On 5/15/06, *Peter I. Hansen* <
<a href="mailto:piha@kvl.dk">piha@kvl.dk</a> <mailto:<a href="mailto:piha@kvl.dk">piha@kvl.dk</a>>> wrote:<br>><br>> Hello<br>><br>> I'm trying to set up a larger carbohydrate for MD in gromacs. I've used
<br>> prodrg for smaller sugars, since pdb2gmx seems to fail due to lack of<br>> residues in the forcefield. But, prodrg fails when the number of atoms<br>> is larger than 300 (and for the beta version, 500 atoms).
<br>> Is there another way to do this setup? I only need poly-alpha-glucose,<br>> so it's just one residue I miss.<br>><br>> thanks, Peter<br>> _______________________________________________
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> 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
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</a><br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>Please don'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't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">
http://www.gromacs.org/mailing_lists/users.php</a><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>