RMSD, RMSF, Rg, and HBond

User discussions
1

GROMACS version: 2020.1
GROMACS modification: Yes

Hello, I wanna ask a question so I have done RMSD, RMSF, Rg and HBond analysis and found this graph as the result

ligand rmsd
ligand rmsd792×612 12.9 KB

So I have found Isoeugenol with yellow line have a lower RMSD value and also RMSF value “BUT” have a higher Rg score and also no HBond has been found

But elemicin with a blue line have a lower Rg score and 2 intermolecular HBond

But for note the low Rg score because the tail was folded during 100-ns simulation.
So I wanna ask which one is the most suitable one to fit at the enzyme’s active site?

and also this enzyme in nature, the active site was found had a hydrophobic condition

Thanks a lot

Regards,
Sony

2

rg (2)
rg (2)792×612 10.2 KB

3

rmsf new
rmsf new792×612 8.35 KB

4

I can’t make sense of all these unlabeled plots, nor can anyone else here. Please provide more context. Are these simulations of protein:ligand complexes? What is your objective? Note that you are unlikely to see major differences in quantities like Rg or RMSF in these situations, and RMSD of the ligand really depends on the quality of the initial pose and the ligand topology, in terms of whether that pose is maintained. The H-bond results are unsurprising given the chemical nature of the compounds.