mmpd_lec4

mmpd_lec4 - "improper dihedrals", such as the...

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20.181 Notes by Mike Yee - October 25, 2006 Dihedrals Protein backbone Where CA is the alpha carbon, C(-1) is the C before the current carbon, etc. Structure of data files for protein backbone: Angle First atom Second Third Fourth φ C -1 N CA C ψ N CA C N +1 ω CA C N +1 CA +1 Now we want to add other stuff. Atom First atom Second Third Fourth Dihedral angle Amide hydrgeon (NH) CA -1 C N NH dih NH Alpha carbon hydrogen (H 1 ) C -1 N CA H 1 dih H1 First carbon on R-group (CB) C -1 N CA CB dih CB Cool. But do we always need to calculate stuff from the inputs? Not for the so-called
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Unformatted text preview: "improper dihedrals", such as the C-CA-N-NH dihedral, or the C-CA-N-NH dihedral, because these are always the same. The "proper" dihedrals (N, CA, C) must be calculated from inputs, but the "improper" dihedrals can be taken from a table. Build order N terminus to C terminus, with increasing i Within the residue, calculate proper dihedrals, take improper dihedrals from a table...
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This note was uploaded on 11/11/2011 for the course BIO 20.010j taught by Professor Lindagriffith during the Spring '06 term at MIT.

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mmpd_lec4 - "improper dihedrals", such as the...

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