Re: [AMBER] CPPTRAJ-Angle between two Helices

From: Daniel Roe <>
Date: Fri, 19 Jan 2018 15:24:10 -0500

Tough to really say what might be going on here without seeing the
system. One thing I like to do in these situations is actually
visualize the vectors themselves. You can do this by writing the
vector data out in 'vectraj' (vector pseudo-trajectory) format, like

vector Helix1 .2018 @2316
vector Helix2 .2316 @22841
writedata vectraj Helix1 Helix2 trajfmt netcdf parmout vectors.parm7

Then you can visualize what the 'vector' commands are actually
calculating and see if those are good representations of your helices.

Hope this helps,


On Fri, Jan 19, 2018 at 1:23 PM, Jag Silwal <> wrote:
> Dear all,
> I want to measure the angle between two helices in a protein for the
> entire simulation (angle Vs time). I found the following guide from Dan and
> I followed it and ran a sample run for one of the helices. I got the
> results and everything but the angle is almost double what I was expecting
> for the entire run.
> So, I think I mightn't be using 'atom mask' properly here. So the two
> helices are connected by a small loop with the turn of about 50 degrees. If
> the starting of one helix is residue 'A' then turns at residue 'B' and
> continues as another helix which ends at residue 'C', can I use the mask as
> follows:
> vector Helix1 .2018 @2316
> vector Helix2 .2316 @22841
> Where, *the numbers are the C-alpha atom number for residues A, B and C.*
> Did I do this right?
> Any insight would be helpful.
> Sincerely,
> Jag
> .......................................................................................................................................
> 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 <>
> Then you would create the vectors:
> vector Helix1 <mask1> <mask2>
> vector Helix2 <mask3> <mask4>
> 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
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
AMBER mailing list
Received on Fri Jan 19 2018 - 12:30:03 PST
Custom Search