The 45a3, 53a5 and 53a6 series of the GROMOS force fields contain carbohydrate parameters. I would advise to use one these (especially because of the treatment of the ring and connecting dihedrals).<br><br>Tsjerk<br><br><div>
<span class="gmail_quote">On 3/29/06, <b class="gmail_sendername">Hugo Verli</b> <<a href="mailto:hverli@cbiot.ufrgs.br">hverli@cbiot.ufrgs.br</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 Andreas,<br><br>As David mentioned, I think that prodrg is the best way to represent<br>carbohydrates in GROMACS. I have simulated heparin and other carbohydrates<br>(sulfated or not) both in solution and complexed with proteins, and had
<br>obtained a high level of accuracy with experimental data, as NMR, X-ray and<br>mutagenesis. The results are fine both with GROMACS force field and with<br>GROMOS96 force field.<br><br>I only suggest a special attention to carbohydrate ring conformation. If it
<br>distort during the simulation I suggest that you fix it in the expected<br>conformation by using improper dihedrals.<br><br>Best regards,<br><br>Hugo Verli.<br><br>-----Mensagem original-----<br>De: <a href="mailto:gmx-users-bounces@gromacs.org">
gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] Em<br>nome de David van der Spoel<br>Enviada em: quarta-feira, 29 de março de 2006 10:10<br>Para: Discussion list for GROMACS users
<br>Assunto: Re: [gmx-users] gromacs with carbohydrates<br><br>Andreas Steffen wrote:<br>> hi,<br>> is there an adequate forcefield in gromacs for dealing with<br>> carbohydrates (cyclodextrin) or do I have to map the atoms to the
<br>> protein atom types?<br>> Thanks in advance!<br>> Andreas.<br>><br>try starting with prodrg<br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
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</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
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