Dear Peter, When using PRODRG to simulate carbohydrates you may have problems to describe the monosaccharide conformations, but it’s a system dependent problem. Considering usual carbohydrates, founded in biological glycosylated proteins, the chair conformation is adequately described (the chair-chair interconversion occurs in time scales far than usual simulations), with no occurrence of twist-boat conformations. If you have some unusual ring conformation, as the iduronic acid in heparin, you can fix the conformation with improper dihedrals and correctly describe the glycosidic linkage geometry, even in complex and highly charged polysaccharides. Such proceeding also makes possible to determine the specific energetic contribution of each monosaccharide conformation upon complexation to target proteins.
One possible problem that you may find is the limited variety of carbohydrate substitution patterns in GROMOS parameterization. Several monosaccharides frequently founded in biological proteins are not included in the force field, so you will need to build your own parameters. It also works fine and, at least for the global geometry of the carbohydrate moiety, you will be capable to reproduce experimental geometry even with a certain level of variation in atomic charges. Best regards, Hugo Verli. -----Mensagem original----- De: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Em nome de Vojtech Spiwok Enviada em: segunda-feira, 15 de maio de 2006 12:30 Para: [email protected] Assunto: [gmx-users] Re: large carbohydrates Dear Peter Unfortunately, carbohydrates require special parametrization of torsions and therefore you should not use PRODRG topologies. Vojtech Spiwok ICT Prague _______________________________________________ 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: 7.1.392 / Virus Database: 268.5.6/339 - Release Date: 14/5/2006 -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.392 / Virus Database: 268.5.6/339 - Release Date: 14/5/2006 _______________________________________________ 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
