Ptraj: dihedral [] [out ] [mass]

Hi,

One thing you can try is calculating the angle between the vectors that run along the helices; this can be done with cpptraj. First, read in your topology and trajectory:

parm MyParm.parm7

trajin MyTraj.nc

Then you would create the vectors:

vector Helix1

vector Helix2

Here, mask1 and mask2 are atom masks defining each end of the first helix and mask3 and mask4 are atom masks defining each end of the second helix. Then you can use the 'vectormath' analysis command to calculate the angle between the vectors:

vectormath vec1 Helix1 vec2 Helix2 dotangle out H1-H2-angle.dat

Hope this helps,

-Dan