How to calculate dihedral (not torsion) angles?
osrisfol at ssmain.uniss.it
Mon Mar 22 08:29:23 EST 1999
Andrew Martin wrote
>OK, now I understand your point :-) I'm not sure of the solution - I
>need to think this through properly, but does it not work out as
>you want if you apply a simple rule like the second atom in your
>sequence is always clockwise to the first?
You got the point. I need a simple rule! :)
Indeed, after some trials, I found the (I hope!)
5132 for the dihedral between 135-123 planes
1354 for the dihedral between 135-345 planes
3516 for the dihedral between 135-561 planes
The first *three* atoms are always clockwise, and the last one
is that preceding the third atom in the ring.
This *seems* to be the rule
searched, but I still have to test it carefully.
>Does the sign matter in any case? For your purposes can you not
>take the modulo (or the square).
The sign is very important, as I have to calculate a complicated
sum of such angles; if one of them assumes a value opposite
to the correct one, the whole sum gets wrong.
>Why not calculate an RMSD? That's
>how one normally gets around the sign problem in cartesian or
>torsional problems... Without knowing more about exactly what
>you want to achieve it's difficult to say :-)
I just need to establish when a cyclohexane is in a chair or
in a twisted-boat conformation, or in a transient form,
and I need the above angles to determine that.
Could you give me more information about RMSD calculations?
My e-mail is: osrisfol at ssmain.uniss.it
Thank you very much for your help.
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