[gmx-users] Regarding g_sgangle index file

[Venkat Reddy]

Dear Gmx-users,
My system has cholesterol molecules and I want to do the orientation
analysis for the cholesterol rings. I found g_sgangle is the suitable tool
to calculate the angle between two cholesterol rings. But the problem is, I
want to do this analysis for my whole system, which has 40 cholesterol
molecules. Whereas I can input either two or three atoms in the g_sgangle
index file. A quick surf through the gmx-archive yielded a suggestion like:

"An index group should contain all (1,2) pairs such that the overall group
size is a multiple of two.  The index group has to be in a particular
order, like 1 2 1 2 etc.,"

Accordingly, I have selected the atoms using
g_select -f *.pdb -s *.tpr -select 'resname CHOL and name R5 R0'   (R5 and
R0 are bead types in CG system)

I got the output index file in the same order.,i.e., R5 R0 R5 R0....etc.
But when I execute g_sgangle, it is saying something wrong with the index
file. How to solve this error?
How to organize the index file in a multiple of 2?

Thank you for your valuable time and concern

-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036