ScdOrderParameter

The Membrane S_CD tool

The Deuterium Order Parameter tool calculates Scd, a parameter typically derived in NMR experiments which reflects the orientational mobility of each C-H bond along the aliphatic lipid tails and thus membrane fluidity.

1. Requirements

Lipid resnames definitions must be correctly set (see Main Window).
Also, see General Requirements.

2. Input

1. Atom selection: atom selection that set the residues (see Resnames at [GUIMainwindow]) to be analyzed. Sterols must be not selected. Default: “not resname CHL1”.
2. Acyl chains: selection of the specific lipid chain to be computed. See console output on a first dummy run for details on MEMBPLUGIN chain assignment.
   If more than one chain is selected, average of carbons with the same assigned index will be shown instead in the generated plot (but not in the .orderparSCD file).
   Important Note: lipids different than phosphoglycerides (e.g. phosphosphingolipids) are likely to have different chain assignments. To avoid spurious average values always check the lipid chain assignment in your system.
3. Leaflets: membrane leaflet to be analysed. “0” and “1” correspond to upper and bottom leaflets, respectively. If both are selected, an average between leaflets will be plotted in the "-SCD vs Frame" plot.
4. From: initial frame number.
5. To: last frame number.
6. Step: "step - 1" frames will be skipped at each iteration. One frame is analysed at each iteration.
7. Output file path: path to the output files, namely a "filename.orderparSCD" file suitable for external analysis, and a "filename.orderparSCD_plot~" temporary file containing -SCD values averaged per frame.

3. Output file format (tabulated)

filename.orderparSCD

Leaflet Frame Lipid Chain ResID    Residue Index Carbon -SCD
0        0  DOPC        2    119        156  2  C22      0.043
0        0  DOPC        2    119        156  3  C23      0.118
0        0  DOPC        2    119        156  4  C24      0.171
0        0  DOPC        2    119        156  5  C25      0.313
0        0  DOPC        2    119        156  6  C26      0.056
0        0  DOPC        2    119        156  7  C27      0.140
0        0  DOPC        2    119        156  8  C28      0.420
0        0  DOPC        2    119        156  9  C29      0.397
0        0  DOPC        2    119        156 10  C210    -0.249
0        0  DOPC        2    119        156 11  C211    -0.062
0        0  DOPC        2    119        156 12  C212     0.468
0        0  DOPC        2    119        156 13  C213     0.444
0        0  DOPC        2    119        156 14  C214     0.486
0        0  DOPC        2    119        156 15  C215     0.401
0        0  DOPC        2    119        156 16  C216     0.465
0        0  DOPC        2    119        156 17  C217     0.354
0        0  DOPC        2    119        156 18  C218    -0.055
0        0  DOPC        2    120        157  2  C22      0.299
0        0  DOPC        2    120        157  3  C23     -0.130
0        0  DOPC        2    120        157  4  C24     -0.177
0        0  DOPC        2    120        157  5  C25     -0.036
0        0  DOPC        2    120        157  6  C26      0.298
0        0  DOPC        2    120        157  7  C27      0.376
0        0  DOPC        2    120        157  8  C28      0.206
0        0  DOPC        2    120        157  9  C29      0.479
0        0  DOPC        2    120        157 10  C210    -0.158
0        0  DOPC        2    120        157 11  C211     0.259
0        0  DOPC        2    120        157 12  C212     0.393
0        0  DOPC        2    120        157 13  C213     0.343
0        0  DOPC        2    120        157 14  C214     0.417
0        0  DOPC        2    120        157 15  C215     0.449
0        0  DOPC        2    120        157 16  C216     0.418
[...]

filename.orderparSCD_plot~

Carbon  -SCD    STD_Error
 1   0.208   0.017
 2   0.272   0.007
 3   0.346   0.006
 4   0.389   0.005
 5   0.408   0.004
 6   0.424   0.004
 7   0.425   0.004
 8   0.426   0.004
 9   0.423   0.004
10   0.416   0.004
11   0.413   0.004
12   0.399   0.004
13   0.376   0.005
14   0.342   0.006
15   0.287   0.007
16   0.171   0.007
17   0.136   0.011
18   0.053   0.009
19   0.016   0.097
20   0.125   0.096
21   0.143   0.086
22   0.062   0.053

• Leaflet: “0” and “1” correspond to upper and bottom leaflets, respectively.
• Frame: frame number.
• Lipid: residue name of each lipid species.
• Chain: acyl chain identifier. Remember to always check the console output on a first dummy run for details for the automatic MEMBPLUGIN's lipid chain assignment.
• ResID: resID of each residue.
• Residue: VMD internal residue number (useful if resID – resname pairs are not unique).
• Index: acyl chain carbon identifier.
• Carbon: acyl chain carbon atom names. In filename.orderparSCD_plot~, this value corresponds to “Index”.
• -SCD: Scd values for each residue. In filename.orderparSCD_plot~, this value is a frame-wise average.
• STD_Error: standard error of each average -SCD.