Hi, When the question is "what's the dynamics of a GlcN chain?", it is quite important to have a proper set of parameters. If the question is "what would a protein do when something resembling a GlcN chain is inserted (e.g. Lysozyme)?" then you may get away using a set of parameters derived from available building blocks with similar groups, using "chemical intuition". In particular, this would apply to simulations aimed at comparing behaviour... at a qualitative level.
Cheers, Tsjerk On Tue, Sep 2, 2008 at 8:45 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > [EMAIL PROTECTED] wrote: >> >> Hi All >> I am trying to analyze the dynamics of polymer of GlcN residues using >> ffG53a6 force field. >> I made a new building block in .rtp file, but I haven´t the charge of some >> atoms. >> Which is the best procedure to obtein new charges? > > For some general information, refer here: > > http://wiki.gromacs.org/index.php/Parameterization > > With empirical force fields like Gromos96, a reasonable starting point is to > identify similar functional groups from other molecules (those that have > been parameterized already), and apply them to your molecule. > > The extent of the validation is up to you, but rigorous verification of the > parameters typically involves some sort of free energy calculations. I have > seen several instances in the literature where investigators have molecules > that are very similar to existing compounds in the force field, and they > have skipped the validation steps. Whether or not that is acceptable is up > to you... > > -Justin > >> Someone has experience about this? >> Any help would be appreciated >> Carmen >> >> _______________________________________________ >> 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 [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > 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 [EMAIL PROTECTED] > 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
