# Why not protein is not come in the selection **URL:** \ **Category:** User discussions\ **Created:** [January 31, 2026, 7:46pm UTC](https://gromacs.bioexcel.eu/t/why-not-protein-is-not-come-in-the-selection/13166 "2026-01-31T19:46:00Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![mondalritam](https://avatars.discourse-cdn.com/v4/letter/m/b77776/32.png) [@mondalritam](https://gromacs.bioexcel.eu/u/mondalritam)\ **Post date:** [January 31, 2026, 7:46pm UTC](https://gromacs.bioexcel.eu/t/why-not-protein-is-not-come-in-the-selection/13166/1 "2026-01-31T19:46:00Z")
gmx rmsf -s em.tpr -f md\_0\_10\_center.xtc -n index.ndx -o rmsf.xvg :-) GROMACS - gmx rmsf, 2026.0 (-: Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /mnt/d/vchemistry2 Command line: gmx rmsf -s em.tpr -f md\_0\_10\_center.xtc -n index.ndx -o rmsf.xvg Reading file em.tpr, VERSION 2026.0 (single precision) Reading file em.tpr, VERSION 2026.0 (single precision) Select group(s) for root mean square calculation Group 0 ( System) has 18 elements Group 1 ( Other) has 18 elements Group 2 ( LIG) has 18 elements Group 3 ( System\_&_!H\*) has 12 elements Select a group: 3 Selected 3: 'System_&\_!H\*’ Last frame 1000 time 10000.000 Can you please help me why not protein or backbone not come in the selection ? Please help me to find the proper command ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [January 31, 2026, 11:00pm UTC](https://gromacs.bioexcel.eu/t/why-not-protein-is-not-come-in-the-selection/13166/2 "2026-01-31T23:00:56Z")
If you pass an index with `-n index.ndx` then you will be prompted with the contents of that index file. Take away that flag and you should get the standard selection options for proteins from GROMACS.