Hi Henry, That would be a bit of a wild west approach. A better approximation would be taking the charges from the backbone amide group, as it is just an amide with on either side aliphatic carbons. Doing it properly is a bit more involved, as for the G53a6 FF you need to choose parameters giving the right free enthalpy of solvation.
Groetjes, Tsjerk On Tue, Nov 22, 2011 at 5:10 PM, Henry Hocking <h.g.hock...@uu.nl> wrote: > Dear all, > Where can I find gromos53a6.ff parameters for pyroglutamate (PCA/ PGLU/ PGA) > ? > Alternatively, given that I have them in amber99.ff and oplsaa.ff is there a > way I could adapt these to gromos53a6.ff? > Can I use, for example, the gromos53a6.ff atom types from glutamine, > add/remove appropriate bonds / angles / impropers and then take the > corresponding charge values from my amber99.ff/aminoacid.rtp file. I assume > that what I've just suggested is the cowboy method and that in reality it is > not that straightforward, right? > Kind regards, > Henry > -------------------------------------------------------- > Henry Hocking, PhD > Utrecht University > Bijvoet Center for Biomolecular Research > Padualaan 8 > 3584 CH Utrecht, The Netherlands > Phone: +31-30-2532875 > Fax: +31-30-253 7623 > E-mail: h.g.hock...@uu.nl > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists