Hi Tsjerk, Sorry i did not supply any information about the enzyme/substrate system. Here, I'm studying the interaction between ester (substrate) and lipase (enzyme). The substrate contains C, O and H atoms. More details are shown in the following address. http://picasaweb.google.com/ZJULiuJi/Experiments#5304476447992943186 Also I'll check the archives for related topics. Thank you so much.
Ji On Thu, Feb 19, 2009 at 6:18 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Ji, > > Well, if others have been there before, you can of course take from > their experience. You haven't mentioned the substrate you're dealing > with, though, so none of us can tell if we can offer the solution to > your problem. First try to search the user list archives and the > topology contribution section of the gromacs site. If that doesn't > give any results, you can post to the user list and see if any of us > has already been there... > > Cheers, > > Tsjerk > > > On Thu, Feb 19, 2009 at 10:35 AM, Ji Liu <zjuli...@gmail.com> wrote: > > Hi Tsjerk, > > > > Thanks a lot. > > Surely I can't modify the force field by my self. It's impossible to me > to > > understand all of things you mentioned. So is it the only way to achieve > my > > purpose? If so, it's so frustrating. I've been trying my best to contact > > with the author of one of my references. He applied several of Gromos 96 > > force field (may be he modified these force field too) to a similar > > enzyme/substrate system, and hope i can get some information from him. > Even > > though, i really eager to get some knowledge from all of gmx-users. > Anyway, > > I'm always grateful for your comment. > > > > Ji > > On Thu, Feb 19, 2009 at 5:09 PM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > >> > >> Hi, > >> > >> > I'm not familiar with > >> > i can't tell myself which > >> > guess i can > >> > I have no idea whether > >> > >> This is the worst possible basis for trying to modify a force field. > >> First get well acquainted with molecular dynamics and the role and > >> whereabouts of force fields. Then you can start thinking of using such > >> knowledge to modify the force field. You will possibly be able to > >> change a force field, but making it produce sensible results is a > >> different thing. > >> > >> Sorry for not telling you what you want to hear. > >> > >> Tsjerk > >> > >> -- > >> Tsjerk A. Wassenaar, Ph.D. > >> Junior UD (post-doc) > >> Biomolecular NMR, Bijvoet Center > >> Utrecht University > >> Padualaan 8 > >> 3584 CH Utrecht > >> The Netherlands > >> P: +31-30-2539931 > >> F: +31-30-2537623 > >> _______________________________________________ > >> gmx-users mailing list gmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before > posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php