I ran a MD simulation for 30 ns using Amber99ff ILDN for protein forcefield and GAFF for ligand forcefield for GKRP and F1P (PDB: 4BB9) consecutively. However, the result shows that the RMSD Complex fluctuates over time until it reach about 27 ns. Also, the RMSD score varies between 50-100 A which very high RMSD score.
Thank you in advance.
Hi, can you please provide the RMSD plot of your simulation? It will be easy to understand.
The complex may not be stable (according to the values mentioned above) or else try performing the MD for 100ns or higher which will give you deeper insight into the stability of the complex.
RMSD score varies between 50-100 A, is something very unusual. You may be doing it something wrong. Also, check the trajectory of the simulations and check the ligand occupancy in the protein binding site. If your RMSD has not converged or stable you need to extend the MD simulation run for more time and check.
- Badges
- Science topic
- Similar topics
- Physical Sciences
- Physical Phenomena
- Luminescence
- Fluorescence