[gmx-users] residue number in secondary structure plot
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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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