# DSSP analysis of a dimer **URL:** \ **Category:** User discussions\ **Created:** [June 25, 2020, 12:18pm UTC](https://gromacs.bioexcel.eu/t/dssp-analysis-of-a-dimer/375 "2020-06-25T12:18:43Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![olga](https://avatars.discourse-cdn.com/v4/letter/o/57b2e6/32.png) [@olga](https://gromacs.bioexcel.eu/u/olga)\ **Post date:** [June 25, 2020, 12:18pm UTC](https://gromacs.bioexcel.eu/t/dssp-analysis-of-a-dimer/375/1 "2020-06-25T12:18:43Z")
GROMACS version:5.1.4 GROMACS modification: No Here post your question Dear gromacs users, Following MD simulation of 700ns, I calculated DSSP analysis by using the **gmx\_mpi do dssp** program. My system contains a dimer that is embedded in a DOPC bilayer. Each chain of the dimer consists of 42 amino acids. To run the do\_dssp command I executed the following: **gmx\_mpi do\_dssp -f 700ns\_whole\_cluster\_center.xtc -s nptno1.tpr -sc scount.xvg -o ss.xpm -tu ns -dt 1** I calculate the dssp only for the “mainchain” (group 5 in gromacs). My questions are regarding the **scount.xvg** and **ss.xpm** files. 1. In the scount.xvg file I got the following table: @ subtitle “Structure = + B-Sheet + B-Bridge + Turn” @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend “Structure” @ s1 legend “Coil” @ s2 legend “B-Sheet” @ s3 legend “B-Bridge” @ s4 legend “Bend” @ s5 legend “Turn” @ s6 legend “3-Helix” @ s7 legend “Chain\_Separator” ``` 0 45 34 38 6 3 1 0 1 1 29 46 18 10 7 1 0 1 2 32 43 24 6 7 2 0 1 3 32 44 22 8 6 2 0 1 699 50 26 42 1 6 7 0 1 700 47 30 42 0 5 5 0 1 ``` # Totals 26405 24431 22301 593 6454 3511 192 701 # SS % 0.45 0.42 0.38 0.01 0.11 0.06 0.00 0.01 What should I do with the “Chain\_Separator”? meaning, from what I have understood this “structure” appears because of the two chains, should I eliminate this structure and recalculate the percentages manually? Moreover, the sum of the values is 0.98 and not 1, why is that? My second question is regarding the **ss.xpm** file (see below). I would expect to get 84 values for the Y-axis which represents the index residue, as I got 84 a.a. However, I got only 83 a.a. I went over the ss.xpm file, and it seems that the do\_dssp did not include the last amino acid (#42), the C-termini, in the calculation. Is it supposed to be like that, eliminating the C-terminus? or do I have any problem? Any ideas on how to solve it? My guess is because of the lack of the oxygens in the “mainchain” group. When I checked which indexes include the group mainchain, it does not contain two oxygens of the carboxylic group of the C-terminus, however, these atoms appear in the coordinate file and also the do-dssp identifies 84 amino acids. So why is that? static char \*gromacs\_xpm[] = { “701 **83** 7 1”, "~ c #FFFFFF " /\* “Coil” \*/, "E c #FF0000 " /\* “B-Sheet” \*/, "B c #000000 " /\* “B-Bridge” \*/, "S c #008000 " /\* “Bend” \*/, "T c #FFFF00 " /\* “Turn” \*/, "G c #808080 " /\* “3-Helix” \*/, "= c #E6E6E6 " /\* “Chain\_Separator” \*/, /\* y-axis: 81 82 **83** \*/ Thank you all in advance. Olga ---
**Author:** ![Irawati](https://avatars.discourse-cdn.com/v4/letter/i/9dc877/32.png) [@Irawati](https://gromacs.bioexcel.eu/u/Irawati)\ **Post date:** [May 20, 2021, 9:35am UTC](https://gromacs.bioexcel.eu/t/dssp-analysis-of-a-dimer/375/2 "2021-05-20T09:35:14Z")
Hi Olga Sorry, my reply is not a solution to your question as such, rather a question. Actually, I also faced the same issue about the number of residues. The terminal residue is missing in the output. Have you realised why it is missing? Also how did you understand that the missing residue is from the C terminal end? I am absolutely puzzled about this. In case if you have some idea I would really appreciate if you share. Thanks in advance.