[gmx-users] Regarding g_sgangle index file

Venkat Reddy venkat4bt at gmail.com
Sun Sep 15 16:05:13 CEST 2013

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

More information about the gromacs.org_gmx-users mailing list