I am trying to perform MD simulations in Amber for a protein-ligand complex (PDB id: 5YY1). The ligand is covalently attached to a side chain atom of an amino acid (for example: ----EDSKL---- a protein chain and the ligand is covalently attached to a side chain atom of K residue) residue. How can I prepare a ligand and receptor file for antechamber and tleap. Means, MD for this complex retaining the covalent bond between protein and ligand. Removing the ligand is creating gaps in the protein. Hoping a positive response.
Thank you.
Define the modified lysine as a new residue, create a model system (an isolated molecule) for this modified lysine, calculate the partial atomic charges (and adjust them to preserve the partial atomic charges of the backbone part of the modified lysine), and add missing bond, angle, and torsion parameters.
Thank you Zhaoxi Sun. I am agree with you. Can you explain it with some example (may be 2PQM) in more detail please.
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