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a rotation of the peptide at the membrane surface
#20778 04/20/09 05:06 PM
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Dear all,

Could you please guide me if it is possible to detect the rotation of the peptide at the membrane interface with the charmm analyis module?
I checked the literature one can get it by measuring the angle between the bilayer normal and the normal to the least squared plane formed by the peptide backbone, in case of peptide orientation in the bilayer.
Could I do same and how to calculate the least squared plane formed by the peptide backbone? thank you very much.

Re: a rotation of the peptide at the membrane surface
beginner #20779 04/20/09 05:55 PM
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rmv Online Content
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As a research tool, just about any analysis one can imagine is possible with CHARMM, either directly, or by exporting the needed data and writing a program.

If the membrane is set up with the Z axis as the bilayer normal, that's a good first step; vector projections on the Z axis can be used to measure rotation. For any vector, if it is normalized to a unit vector, the z component is the cosine of the angle it makes with the Z axis.

Choosing the right vectors for the peptide can pose a challenge, however, and the least-squares plane normal may only be appropriate for a flat peptide, such as a beta hairpin config. For a helix, that is probably not a good choice. You must first establish how much the peptide conformation changes during the simulation in order to pick the right vector(s).

There are a number of ways to define vectors within CORREL, and a couple more COOR commands, such as COOR LSQP and COOR HELIX

Re: a rotation of the peptide at the membrane surface
rmv #20780 04/28/09 02:33 PM
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thank you very much, rick. I very appreciate your time. However, I have no idea how to detect the rotation around that axis.
thank you.

Re: a rotation of the peptide at the membrane surface
beginner #20781 04/28/09 04:44 PM
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Rotation around an axis typically requires vector(s) orthogonal to the axis; it might be more useful to monitor selected Calpha --> Cbeta bond vectors.


Moderated by  lennart, rmv 

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