Hello all,
I am doing molecular dynamics simulation using gromacs for protein-ligand interaction. The simulation is going well. However, the crystal structure of protein have ANISOU instead of ATOM (shown in figure below). I wonder whether I need to rerun the simulation after remove the ANISOU from PDB.
If the simulation is running OK, the program most likely simply ignores the ANISOU records, as it ignores the B-Factors.
Nur Farhana Mustafa As Annemarie Honegger suggested if the simulation runs okay, then fine. If you face some abnormal fluctuations or deviations in the output graph, then you should consider removing them. I would suggest you to go with small time frame simulations to understand the motion.
You can use my code from github to remove anisou and select the chain of your interest for docking/simulations.
https://github.com/thirumal-kumar/Protein_NoANISOU_Chain_Selection/blob/main/Protein_NoANISOU_Chain_Selection.py
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