In fact, I want to make an isopeptide bond. On Mon, May 11, 2015 at 11:04 PM, Andrew Bostick <andrew.bosti...@gmail.com> wrote:
> Dear gromacs users > > I have experience in MD simulation of protein and peptides by gromos force > field. > > Now I am working on a new project in which I should connect two peptides > (based on experimental data) to obtain one new peptide. This connection is > as follows: > > CD atom of GLU residue from peptide 1 and NZ atom of LYS residue from > peptide 2. > > 1) How to make this connection (which software) to gromacs recognize this > new state. > > 2) Should I need to change force field parameters? > > 3) Should I define new residue containing Glu-Lys? > > Any help will highly appreciated. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
