[gmx-users] residue number in secondary structure plot
compbioph at gmail.com
Sun Sep 10 06:38:53 CEST 2017
Than you Justin. I used CHARMM force field.
On Sat, Sep 9, 2017 at 10:38 PM, Justin Lemkul <jalemkul at 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 A. Lemkul, Ph.D.
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> Virginia Tech Department of Biochemistry
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