Mapping for stearic tail and inositol

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Mel
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7 years 10 months ago #5667 by Mel

Mapping for stearic tail and inositol was created by Mel

Hi,

I already asked this question for linoleic and oleic tails, but what is the AA mapping for the stearic (18:0) tail? As with palmitic acid it is mapped to 4 beads, but I can't figure out which beads have more heavy atoms than others?

Another issue is with glycolipids with an inositol head. From the Paper (Lopez et al. 2013) one can see in the figure more or less how the beads are mapped but I want to be 100% sure.

Thanks again for your help

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helgi
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7 years 10 months ago #5687 by helgi

Replied by helgi on topic Mapping for stearic tail and inositol

Martini is based on a building block approach and getting overall physiochemical properties correct. Therefore, there is not a unique correct mapping (e.g. multiple atomistic tails map to the same CG tail). For a “good” mapping of the C18:0 steric tail you can use the same heavy atom placement as in the oleic tail.

And for the inositol we will have backmapping files online some time later this summer, but the inositol mapping would be:
[ C1 ]
C1 C2 O2
[ C2 ]
O4 C4 C3 O3
[ C3 ]
C5 O5 C6 O6
e.g. x2 beads with x2 C and x2 O and the third bead is missing the last O due to the linking with the PO4.

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Mel
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7 years 8 months ago #5748 by Mel

Replied by Mel on topic Mapping for stearic tail and inositol

Thanks for the help, Helgi. I will use these mappings for my simulations.

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Mapping for stearic tail and inositol