[gmx-users] residue number in secondary structure plot

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
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