How to define backbone group in RNA

User discussions
1

GROMACS version: 20.3
GROMACS modification: No
Here post your question
I am currently performing a molecular dynamic simulation on RNA. while performing analysis of (FOR EXAMPLE RMSD) , during command execution i am not finding any option of selecting BACKBONE GROUP as in case of protein analysis. please suggest me as to what should I perform to obtain backbone group. if in case there isn’t an option of selecting backbone group in RNA analysis then what should be done to obtain similar results.

Thanks and Regards
Shailesh Mani Tripathi
Central University of Rajasthan, Rajasthan
India
Email- 2019mppc005@gmail.com

2

Hi,
You can generate an index file (ndx file), where you define a group containing the backbone atoms of RNA. Then you can give this index file as input to other gmx tools using the option -n {filename}.ndx

To generate an index file for the backbone atom, you can use gmx make_ndx

Best regards
Alessandra