VMD-L Mailing List

From: Aiswarya (aiswarya.pawar_at_gmail.com)
Date: Thu Oct 09 2014 - 13:32:55 CDT

Dear Users,
Am trying to calculate rotational angle for a given 4 atoms, am getting the value of angle correct but its not differentiating between +ve and -ve. Ie if the angle between 4 atoms is -177 degrees am getting 177 degree, and there is no -ve sign to it. Below is the script i have used.

> # Computes the dihedral angle of a bond
>
> set coord1 [lindex [[atomselect top "index 86" ] get {x y z}] 0]
> set coord2 [lindex [[atomselect top "index 89" ] get {x y z}] 0]
> set coord3 [lindex [[atomselect top "index 75" ] get {x y z}] 0]
> set coord4 [lindex [[atomselect top "index 23"] get {x y z}] 0]
> set v1 [vecsub $coord1 $coord2]
> set v2 [vecsub $coord3 $coord2]
> set v3 [vecsub $coord4 $coord3]
>
> set cross1 [vecnorm [veccross $v2 $v1]]
> set cross2 [vecnorm [veccross $v2 $v3]]
> set cos [vecdot $cross1 $cross2]
> set rotvec [veccross $cross1 $cross2]
> set sin [veclength $rotvec]
> set angle [expr atan2($sin,$cos)*(180.0/3.14)]
> return $angle

Please someone tell me were am going wrong.

Thank you so much,
Aiswarya