I'm new to Molecular Dynamics and I have some doubts about the following things that I have done:
I am studying an enzyme which is not in the PDB site. So I performed homology modeling using Modeler. I modeled two structure using two approaches: 1) single-template 2) multiple templates generated from Modeler. (Q: I didn't introduce any disulphide bonds or any additional info, just based on the Modeler output, is it ok?)
I have used SAVS to evaluate both the models. For the single-template approach, i obtained 91.2 core, 6.6 allow, 1.0 generous, 1.2 disallowed (Ramachandran Plot) and 89.1 core, 9.4 allow, 0.8 generous, 0.6 disallowed for the multiple-template approach. (Q: can I conclude that the second model is the better one?)
Next, I tried to perform energy minimization using GROMACS. Then I did MD simulation for 10ns, but the RMSD and radius of gyration for both the models did not converge (keeps increasing).
Next step I'm suppose to do is Docking this enzyme to a ligand. Can I proceed with the structure (second model)?
Please advice. Any suggestions are very much appreciated. Thank you in advance!