Why can’t we find Radius of gyration of RNA… I know it do not have alpha-helices or beta-sheets but it does have stems and loops… Why is it not possible to find Rg for it… Please help me understand it…
If you’re having a specific problem using a GROMACS tool, please be more specific and provide your actual command. You can compute Rg for any selection of any atoms; it has nothing to do with whether something is a protein or not. gmx gyrate will calculate the value for any selection of atoms you make.
Sir actually I am working on RNA-SRV-1 and i used following command for Rg calculation:
gmx rama -f 0308_pull1_nojump.xtc -s 0308_pull1.tpr -o ramachandran1.xvg
But all i got blank graph of ramachandran
A Ramachandran plot is specifically for proteins as it is a surface of (φ,ψ) pairs. It can’t be used for RNA. You asked about radius of gyration, which is computed by gmx gyrate. It looks like you’re simply using the wrong tool.
Ohkk… Now I got it… Thank you…