Than you Justin. I used CHARMM force field. On Sat, Sep 9, 2017 at 10:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 9/9/17 1:58 PM, Emran Heshmati wrote: > >> Dear Gromacs users >> I performed a md simulation on apeptide fragment consist of 16 aa . when I >> analysed its secondary structure content using "gmx do_dssp " command, >> there was only 15 aa in y-axis in resultig *.eps file format. can anyone >> explain this controversy. >> > What force field did you use? IIRC, the code doesn't recognize CHARMM > C-terminal oxygen atoms correctly so the program ignores them. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > 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.
