Hello!
I want to restraint my ligand with a protein in Gromacs.
According the reference, specific atoms of the ligand are joined with the protein:
R1 interacts with 459-462 amino acid residues
R7-R8 interacts with 480-486 amino acid residues
R7 interacts with 498-502 amino acid residues
R2 interacts with 86-91 amino acid residues
Carboxylate interacts with 86-91 amino acid residues
In this case, should I use genres or another type of restraint?
When I observed the trayectories of molecular dynamic, the drug is out of place and moving.
Thanks very much.
Half-harmonic distance restraint (between an atom of the ligand and an atom of the protein), or harmonic positional restraint to initial atomic positions or to the center of mass or to the geometrical center of the ligand.
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