Dear researcher,
I did the molecular dynamic simulation of a protein till 50 ns. My protein got the equillibriation state after 10 ns. I took the last 10 ns trajectory and predicted 10 structures. All the structures are good in various protein validation tools except Ramachandran plot.
In without MD structure i got the 87% residues lies in the allowed reigon but after MD the residues are fall down and it is only 75%.
I also attached both the ramachandran plot files
please suggest me how i can improve the Ramachandran plot
Did you energy-minimize the selected MD structures before calculating the phi and psi angles?
MD simulation shouldn't necessarily be explained by torsion angles as conformation with the most allowed angles doesn't have to be the accurate structure.
Dear Martin sir
I did not do the energy minimization after MD. are it is required.
How was the "equilibrated state" determined?
How many MD simulations were performed---just one? If so, run multiple short MD simulations using different initial conditions (e.g., the initial velocities).
What was the procedure for selecting 10 structures from the 10-ns MD simulation---a clustering analysis?
Why was 40 ns of the production MD simulation omitted?
What is the purpose of the MD simulation---to refine an in silico protein model? If so, run cooling MD simulations for selected MD snapshots (or representative structure of each cluster) toward 0 K and energy-minimize the final structures.
Dear Rohit
If you just want to improve Ramchandran plot try this : http://zhanglab.ccmb.med.umich.edu/ModRefiner/
Just upload your PDB file
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