[AMBER] CPPTRAJ-Angle between two Helices

From: Jag Silwal <jagsilwal.gmail.com>
Date: Fri, 19 Jan 2018 13:23:06 -0500

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 MyTraj.nc <https://www.researchgate.net/deref/http%3A%2F%2FMyTraj.nc>
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
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Received on Fri Jan 19 2018 - 10:30:02 PST
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