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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
