[gmx-users] Why "do_dssp" gives one more residue?

[Qinghua Liao]

Hello,

Maybe you have two chains in your system, then there should be one for 
chain separator.


Best,
Qinghua

On 02/21/2018 06:20 PM, ZHANG Cheng wrote:
> Dear Gromacs,
> My protein only has 442 residues. After running
>
>
> gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns
>
>
> In the ss.xpm file, I got 443 numberings, i.e. y-axis is numbered from 1 to 443.
>
>
> Can I ask why is that? Should I just ignore the 443th data?
>
>
> Yours sincerely
> Cheng
>
>
> Here is some content copied from the ss.xpm file:
>
>
> /* x-label: "Time (ns)" */
> /* y-label: "Residue" */
> /* type:    "Discrete" */
> static char *gromacs_xpm[] = {
> "317 443   8 1",
>
>
>
> ... ...
>
>
> /* y-axis:  401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 */