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

[ZHANG Cheng]

Dear Justin,
Thank you. But it does not make sense to me. Do you know if separator line is always all the ~ ? If the separator line is following the 214th residue, the 215th residue should be the separator line, but why the 215th residue contains the secondary structure?


You can find my files at
https://1drv.ms/f/s!AjIs-W_id1LzpOsT2Dktn9hIO7-eNA


If you use a text editor, 
The 214th residue: line 248
The 215th residue: line 249


The pdb file (bfac.pdb) after the simulation is also in the link (without the chain ID). 


The original pdb I use contains two chains. After running "gmx pdb2gmx  -f protein.pdb -o protein_processed.gro -water spce  -inter  -ignh -merge interactive", the two chains are merged to keep the inter-chain disulfide bond, and also the chain ID has been lost since then.


Thank you.


Yours sincerely
Cheng




------------------ Original ------------------
From:  "ZHANG Cheng"<272699575 at qq.com>;
Date:  Thu, Feb 22, 2018 01:34 AM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;

Subject:  Re: Why "do_dssp" gives one more residue?



Dear Qinghua,
Yes, exactly! But the numbering is:


1-214: first chain
215-442: second chain


However, for the secondary structure codes:


214th: 
"TTSTSSSTSSSTTSTSS~SSSTTTTTTTTSSTTTTTTTTTTTTSTSSSTSTTTTTTTTTTTTTTTTTTTTTTTSTTTTTSTSTTTTTTTTTTTTTTTTTT~SS~SSSTSTTTSSSSSSTTTSSSSSSTSSTTTSTTTTTTTTTTTTTTTTSGSTTSTSTTTTSSSSSSTTTTSSSSTSSTTTTTSTTTTTTTTTTTTSTTSSSSSSTSTTSSSTSSTTSSSSTTTEEBSSESSSSBSSTSSTSEESTSSSSSTSTSTSTTTSSSTTTSTTTTTSTSSTSTTTTTTSSTTTTTTTTSTTTESET~~~SSS~SSS~~S~",


215th:
"TTST~~~TSSSTTST~~~~SSTTTTTTTTSSTTTTTTTTTTTTSTSSSTSTTTTTTTTTTTTTTTTTTTTTTTSTTTTTSTSTTTTTTTTTTTTTTTTTT~~SSSS~TSTTTSSSS~STTTSSSSSSTSSTTTSTTTTTTTTTTTTTTTTSGSTTSTSTTTT~~~~~STTTT~SSSTSSTTTTTSTTTTTTTTSTTTSTTSSSSSSTSTTSSSTSSTTSSSSTTTSSSSSSSSSSSSSTSSTSSSSTSSSSSTSTSTSTTTSSSTTTSTTTTTSTSSTSTTTTTTSSTTTTTTTTSTTT~SSS~S~~~~~~~~~~~~",


442th:
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~BBBBB~~BBB~BB~~~~~BBB~B~~~B~~B~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~~~~~~~~~~~~~~~~~~~~B~B~~~~~~B~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~",


443th: "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"




Do you think the 443th line is the separator? So ignore the 443th line?






------------------ Original ------------------
From:  "ZHANG Cheng"<272699575 at qq.com>;
Date:  Thu, Feb 22, 2018 01:20 AM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;"ZHANG Cheng"<272699575 at qq.com>;

Subject:  Why "do_dssp" gives one more residue?



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 */