AMBER Archive (2004)

Subject: AMBER: torsion angles

From: John (john.dalmaris_at_imperial.ac.uk)
Date: Fri May 28 2004 - 18:02:04 CDT

Hello,

 

I have a question regarding the way Amber calculates torsion angles. As far
as I know Amber reads peptides the conventional way (N to C terminal). I
have created a peptide from the C to the N terminal. I would imagine that
amber is still reading from left to right without realising that now C
precedes and N follows. If in the conventional way amber is using a
right-handed screw operation to calculate the angle would a left-handed
screw operation give the correct value in the C to N case?

 

In other words will an inversion of the sign provide a consistent way in
describing the N to C and C to N peptides?

 

Thanks in advance for any comment.

 

John

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