Dear Andreas, As David mentioned, I think that prodrg is the best way to represent carbohydrates in GROMACS. I have simulated heparin and other carbohydrates (sulfated or not) both in solution and complexed with proteins, and had obtained a high level of accuracy with experimental data, as NMR, X-ray and mutagenesis. The results are fine both with GROMACS force field and with GROMOS96 force field.
I only suggest a special attention to carbohydrate ring conformation. If it distort during the simulation I suggest that you fix it in the expected conformation by using improper dihedrals. Best regards, Hugo Verli. -----Mensagem original----- De: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Em nome de David van der Spoel Enviada em: quarta-feira, 29 de março de 2006 10:10 Para: Discussion list for GROMACS users Assunto: Re: [gmx-users] gromacs with carbohydrates Andreas Steffen wrote: > hi, > is there an adequate forcefield in gromacs for dealing with > carbohydrates (cyclodextrin) or do I have to map the atoms to the > protein atom types? > Thanks in advance! > Andreas. > try starting with prodrg -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.1.385 / Virus Database: 268.3.3/296 - Release Date: 29/3/2006 -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.385 / Virus Database: 268.3.3/296 - Release Date: 29/3/2006 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
