Command line RMSF and Rg?

User discussions
1

In Gromacs, how can i run the RMSF of the complex Protein-ligand what command should i use
Right now i’m using this one but gmx rmsf -s md.tpr -f md_center.xtc -o rmsf-lig.xvg -res but i can only selct one group :

Group     0 (         System) has 1518398 elements
Group     1 (        Protein) has  5136 elements
Group     2 (      Protein-H) has  2676 elements
Group     3 (        C-alpha) has   338 elements
Group     4 (       Backbone) has  1014 elements
Group     5 (      MainChain) has  1354 elements
Group     6 (   MainChain+Cb) has  1660 elements
Group     7 (    MainChain+H) has  1674 elements
Group     8 (      SideChain) has  3462 elements
Group     9 (    SideChain-H) has  1322 elements
Group    10 (    Prot-Masses) has  5136 elements
Group    11 (    non-Protein) has 1513262 elements
Group    12 (            Ion) has    22 elements
Group    13 (          Other) has    40 elements
Group    14 (             ZN) has     4 elements
Group    15 (             CA) has     2 elements
Group    16 (            LIG) has    40 elements
Group    17 (             NA) has    16 elements
Group    18 (          Water) has 1513200 elements
Group    19 (            SOL) has 1513200 elements
Group    20 (      non-Water) has  5198 elements
Group    21 ( Water_and_ions) has 1513222 elements

What command should i run in order to get the rsmf of my complex Protein-Ligand idem for Rg parameter

2

You need to create a selection group that contains both the protein and the ligand. Now you are not using any index file at all as input to gmx rmsf, the selection groups are automatically determined from the tpr file. You can use gmx make_ndx to create a file with custom selection groups.

3

Yes, it worked as you suggested, but I noticed that the RMSF of the protein-ligand complex is not very insightful on its own because the ligand only generates a single peak, which is expected. For the RMSF in the context of a scientific article to analyze residues, should I select the protein or the backbone? For the RMSD, I’m choosing the entire complex, and I plan to do the same for hydrogen bonds, radius of gyration (Rg), and SASA.