DSSP analysis of a dimer

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1

GROMACS version:5.1.4
GROMACS modification: No
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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

2

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.