Radius Of Gyration Using Gromacs

Question

[cooolgauravpandey]

Hello, I wanted to calculate the radius of gyration for each amino acid, so i have made a PDB file having all 20 amino acid using Ribosome tool(from Roselabs), and have used gromacs for calculation their radius of gyration, but i am not able to figure out which of the following options is correct: Group 0 ( System) has 2640 elements Group 1 ( Protein) has 327 elements Group 2 ( Protein-H) has 168 elements Group 3 ( C-alpha) has 20 elements Group 4 ( Backbone) has 60 elements Group 5 ( MainChain) has 79 elements Group 6 ( MainChain+Cb) has 98 elements Group 7 ( MainChain+H) has 100 elements Group 8 ( SideChain) has 227 elements Group 9 ( SideChain-H) has 89 elements Group 10 ( Prot-Masses) has 327 elements Group 11 ( non-Protein) has 2313 elements Group 12 ( Water) has 2313 elements Group 13 ( SOL) has 2313 elements Group 14 ( non-Water) has 327 elements which one is correct?

Answer 1

[Hub]

You need to create a special index file (with the command make_ndx) with one group per residue.

Then, launch the calculation of the radius of gyration with this index file for each amino acid.

[cooolgauravpandey]

THANKS A LOT..:)