[gmx-users] residue number in secondary structure plot

Justin Lemkul jalemkul at vt.edu
Sat Sep 9 20:09:01 CEST 2017

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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list