# Protein-ligand rmsf graph strange **URL:** \ **Category:** User discussions\ **Created:** [November 3, 2022, 9:22am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-rmsf-graph-strange/5161 "2022-11-03T09:22:25Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![imrbay](https://avatars.discourse-cdn.com/v4/letter/i/67e7ee/32.png) [@imrbay](https://gromacs.bioexcel.eu/u/imrbay)\ **Post date:** [November 3, 2022, 9:22am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-rmsf-graph-strange/5161/1 "2022-11-03T09:22:25Z")
GROMACS version:2020 GROMACS modification: Yes/No Here post your question ![rmsf3](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/1f3a2845fac5d54db7ba5dc80ce73c5777beceff.png) gmx rmsf -s step5.tpr -f new.xtc -o yeni\_back.xvg -res -oq bfactor1.pdb used this inorder to calculation rmsf of protein backbone ı coudnt understand why my rmsf graph is so weird ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [November 3, 2022, 10:41am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-rmsf-graph-strange/5161/2 "2022-11-03T10:41:00Z")
Presumably you have a dimer, each chain of which is numbered from 1. The output RMSF graph numbers the residues exactly as they are in the topology, then XmGrace just does an odd thing where it tries to connect the different data sets, hence you get that odd line. If you have multiple chains, it is generally a good idea to analyze them separately so the data are in different files that can be plotted more conveniently. ---
**Author:** ![imrbay](https://avatars.discourse-cdn.com/v4/letter/i/67e7ee/32.png) [@imrbay](https://gromacs.bioexcel.eu/u/imrbay)\ **Post date:** [November 3, 2022, 11:38am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-rmsf-graph-strange/5161/3 "2022-11-03T11:38:59Z")
gmx make\_ndx -f step3\_input.pdb -o index1.ndx The problem is that chain A Found 0 atoms with chain identifier A do you have any suggestion Group is empty Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 696 Protein residues There are: 85301 Other residues Analysing Protein… Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups… 0 System : 266871 atoms 1 Protein : 10998 atoms 2 Protein-H : 5506 atoms 3 C-alpha : 696 atoms 4 Backbone : 2088 atoms 5 MainChain : 2782 atoms 6 MainChain+Cb : 3434 atoms 7 MainChain+H : 3448 atoms 8 SideChain : 7550 atoms 9 SideChain-H : 2724 atoms 10 Prot-Masses : 10998 atoms 11 non-Protein : 255873 atoms 12 Other : 255873 atoms 13 UNK : 21 atoms 14 SOD : 24 atoms 15 TIP3 : 255828 atoms nr : group ‘!’: not ‘name’ nr name ‘splitch’ nr Enter: list groups ‘a’: atom ‘&’: and ‘del’ nr ‘splitres’ nr ‘l’: list residues ‘t’: atom type ‘|’: or ‘keep’ nr ‘splitat’ nr ‘h’: help ‘r’: residue ‘res’ nr ‘chain’ char “name”: group ‘case’: case sensitive ‘q’: save and quit ‘ri’: residue index chain A Found 0 atoms with chain identifier A Group is empty ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [November 3, 2022, 1:01pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-rmsf-graph-strange/5161/4 "2022-11-03T13:01:39Z")
You can only select by chain identifier if they are actually present in the input PDB file. Presumably your file simply doesn’t have identifiers. Select by ranges of atom numbers if needed, or provide a file that has chain identifiers in it. ---
**Author:** ![imrbay](https://avatars.discourse-cdn.com/v4/letter/i/67e7ee/32.png) [@imrbay](https://gromacs.bioexcel.eu/u/imrbay)\ **Post date:** [November 3, 2022, 1:26pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-rmsf-graph-strange/5161/5 "2022-11-03T13:26:25Z")
chain A consist of 1-348 residues but identified my pdp file so I created r 1-348 & a CA 20 r\_1-348\_&_CA : 694 atoms 0 System : 266871 atoms 1 Protein : 10998 atoms 2 Protein-H : 5506 atoms 3 C-alpha : 696 atoms 4 Backbone : 2088 atoms 5 MainChain : 2782 atoms 6 MainChain+Cb : 3434 atoms 7 MainChain+H : 3448 atoms 8 SideChain : 7550 atoms 9 SideChain-H : 2724 atoms 10 Prot-Masses : 10998 atoms 11 non-Protein : 255873 atoms 12 Other : 255873 atoms 13 UNK : 21 atoms 14 SOD : 24 atoms 15 TIP3 : 255828 atoms 16 chain : 12034 atoms 17 chain : 1044 atoms 18 A : 12034 atoms 19 ch : 12034 atoms 20 r\_1-348_&\_CA : 694 atoms gmx rmsf -s step5.tpr -f new.xtc -n index1.ndx -o CA1\_rmsdf.xvg -res then my graph is same error ![5](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/7/73b7ff44bbf35ba22d58ba142e0a4267a73e6f93.png) what I did something wrong,the mistakes on my created group I just want to select 1-348 residues from the residues,I want to choose CA atoms,so I created r 1-348 & a CA this is wrong ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [November 3, 2022, 1:38pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-rmsf-graph-strange/5161/6 "2022-11-03T13:38:43Z")
If your two chains use the same residue numbers (which is the origin of the problem in the RMSF graph, as I noted above), creating a new index group using residue numbers will not yield any productive solution, since both chains will be selected. As I said, use **atom** numbers to create the groups.