[gmx-users] PROTEIN FOLDING

[Nikhil Maroli]

After MD simulation of protein-ligand complex for 5ns, can we view protein
folding?

mostly, NO

Search what time range 'protein folding' is happening.

How to do it?

I want to ascertain if there is any conformation change in protein where
the ligand binds. Is it possible?


You might want to do PCA, RMSD and DSSP

We observe hydrogen bonds through molecular docking. Hence, I want to make
observation through MD simulation which is not obtained through docking.


gmx hbond

Can someone help me regarding this?


i really wondering what is possible in 5 ns simulation time, you may
try to extend it up to 100 ns or atleast a 50 ns.

Thank you very much in advance.