You can choose different termini by setting the option term (-term) to pdb2gmx.
The ff gromos 53a6 has a strong tendency to destabilize alpha helices and favors sheets. If you like to stick to gromos ff you need to switch to the 54a7 more recent version to which a rectification of this bias has been attempt. > On Dec 7, 2013, at 14:11, Shine A <shin...@iisertvm.ac.in> wrote: > > Sir, > > I am using MD to study the folding of peptides. Now I want to > modify N terminal of the peptide with acetyl group and C terminus with > amide group.How Can I do this? What are the changes I should made in > various files? Gromos96 53a6 is using for simulation. > > > > Thank in advance > -- > 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. -- 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.
