in complex with a ligand. This tutorial focuses specifically on issues related to dealing with the ligand, assuming that the user is familiar with basic GROMACS operations and the contents of a topology. If this is not the case, please refer toa more basic tutorialbefore attempting this one. ...
GROMACS Tutorial Step Two: Prepare the Ligand Topology We must now deal with the ligand. But how does one come up with parameters for some species that the force field does not automatically recognize? Proper treatment of ligands is one of the most challenging tasks in molecular simulation. For...
Previously, it was shown that small-molecule ligand bindings of trapped proteins could be detected using cylindrical ClyA nanopores17,18,38. In a ClyA nanopore, the ligand-induced conformational change of protein results in movement in its residence site within the pore, thereby inducing differential...
MD simulations were carried out for free HUSpm and its complexes with DS14 DNA (Supplementary TableS4) and BDF4 (Supplementary TableS3) using the GROMACS 2019.2 simulation package50. OPLS-AA/L force field51was used with a rectangular model box with a minimum distance from the solute molecule ...