i have modelled one protein by using modeller, after docking protein with suitable ligand, it is interacting with five amino acid residues, then i submitted that complex to 20 ns simulation (Gromacs). after completion of simulation i extracted protein-ligand complex from *trr and *tpr files, it is showing interaction with five amino acid residues but two amino acid residues are different from initial docked structure? what might be the reason for this? is it acceptable?
This paper may give the answer to your queries.
Structural and mechanistic analysis of engineered trichodiene ...
www.tandfonline.com/doi/pdf/10.1080/07391102.2015.1073632
Please keep in mind that the time scale of a molecular dynamics simulation is very short compared to the time scale of, say, a single catalytic turnover of most enzymes. What you see happening in 20 ns may not fully represent what happens over that longer time scale.
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