On Mon, 2008-07-21 at 11:49 -0600, Travis Craddock wrote: > Hello all, > > I am trying to make an addition to mu ffG43a1.rtp file for the molecule GDP. > I have read the entry: > > http://www.gromacs.org/pipermail/gmx-users/2007-December/031139.html > > which gives the topology for GTP. I would like to know how the parameters for > the GTP topology were found so that I may extend them to GDP.
You should delete the beta-phosphate and fix the bonds, angles, etc. For MM calculations this approximation is ok: GDP beta phosphate = GTP gamma phosphate Greetings, Christian. > > Thanks, > Travis > > > Travis Craddock > Department of Physics > University of Alberta > > _______________________________________________ > gmx-users mailing list [email protected] > 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 -- M. Sc. Christian Seifert Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de _______________________________________________ gmx-users mailing list [email protected] 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
