normal Backbone dihedrals at ends of helix

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1 year 4 weeks ago - 1 year 4 weeks ago #8982 by slall
My question is to seek some more clarity about backbone dihedral angles for maintaining secondary structure in Martini, specifically, at the ends of helices. When one uses martinize on isolated helices, it assigns "1" and "2" denomination at helix start and end. But, it is not clear to me whether these assignments have implications for their secondary structure.

Simply, as we know backbone dihedrals in Martini require 4 consecutive backbone beads, so what happens at the first three and the last three residues?
Last edit: 1 year 4 weeks ago by slall. Reason: clarity in title

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11 months 2 weeks ago #9077 by paulocts
Replied by paulocts on topic Backbone dihedrals at ends of helix
Hi

The answer can depends of the version of Martini you are using. In Martini 2.2, secondary structures assigned as "1", "2" or "H" are consider to be "helix", with all bonded parameters reflecting this choice. There is no difference in the bonded parameters if the bead is assigned as H, 1 or 2. However, you have differences in bead assignment of the backbone (BB) bead. "1" and "2" represents the terminals of the helix which will be represented by "Na" and "Nd" beads. These bead are more hydrophilic than "N0", which is the default choice for helices (i.e. "central" BB beads there). So, in conclusion, the implications for the secondary structure in Martini 2.2 are more related to how the terminals interacts with the environment.

In Martini 3, the BB bead type does not change with the secondary structure. But, as the default choice in the model is to add side chain corrections, you may have differences in the dihedrals for the ends of the helices. However, this do not depends of the secondary structure assignment. It is actually related with your atomistic structure use as reference in Martinize2.

Best,

Paulo

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