To update the topic, I tried to compute the angle of the helix rotation
based on its principal axe via the following tleap commands:
principal :residues_of_helix dorotation
vector v1 principal :residues_of_helix out VectorRot.xvg
that produced multicolumn data for each frame:
#Frame v1
0.5000 1.0000 -0.0000 -0.0000 12.0711 24.3398 164.1300
1.0000 1.0000 -0.0000 0.0000 10.9248 25.4559 164.0409
1.5000 1.0000 -0.0000 -0.0000 -7.5949 -25.9691 164.1484
2.0000 1.0000 -0.0000 0.0000 13.1183 25.0266 163.9462
2.5000 1.0000 -0.0000 0.0000 -8.8657 -26.2054 164.0471
3.0000 1.0000 -0.0000 -0.0000 11.3225 24.5876 164.1464
3.5000 1.0000 0.0000 0.0000 13.8911 24.1139 164.0193
Does the value closer to 160 belong to this rotational angle ?
Many thanks in advance !
Cheers
Enrico
Il giorno mer 26 giu 2024 alle ore 09:14 Enrico Martinez <
jmsstarlight.gmail.com> ha scritto:
> Dear Amber users !
>
> Dealing with the modeling of transmembrane peptide, I need to clarify
> possible rotation of the helix inside the membrane containing cholesterol.
> I have already computed the RMSD of the helix but it did not provide any
> clues about its rotation.What commands from the cpptraj could be useful for
> such analysis using the specified atom selection ?
>
> Many thanks in advance
>
> Best wishes,
>
> Enrico
>
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Received on Tue Jul 02 2024 - 09:00:02 PDT
