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Re: Switch in conformation from D amino acid to L amino acid
Rakesh #38172 01/21/21 05:03 PM
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I'm not exactly sure what you mean by the quadrant numbers, it's not a definition I'm familiar with.

I've only used CHARMM to compute the improper dihedral, but it's just straightforward geometry for two planes defined by 3 atoms, with 2 common atoms (N,C) defining the axis.


Rick Venable
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Re: Switch in conformation from D amino acid to L amino acid
Rakesh #38174 01/21/21 06:13 PM
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You must be acquainted about Ramachandran plot.

There are 4 quadrant right, so I am saying that some frames of simulation of D RESIDUE comes in second quadrant which is disallowed region according to GN ramachandran for D amino acid

Re: Switch in conformation from D amino acid to L amino acid
Rakesh #38175 01/21/21 06:52 PM
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I am well aware of the plot and quadrants, but not the precise definition of which quadrant is numbered 1, 2, etc.; do you have a reference (URL or citation) for the numbering scheme?


Rick Venable
computational chemist

Re: Switch in conformation from D amino acid to L amino acid
Rakesh #38176 01/21/21 08:13 PM
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https://images.app.goo.gl/kTswwMCbzfbWi3gN6

https://images.app.goo.gl/w42HjjYV9Ajuiyyr6


I have attached a URL please have a look. First one is allowed region for L and D residue

Second one state the quadrant numbering

Quadrant nomenclature or numbering of ramachandran plot is same as Cartesian coordinate

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