[gmx-users] Preparation protein-ligand complex

[James Starlight]

Dear Gromacs Users!


During preparation of the protein-ligand complex (manual placement of
the ligand into the ligand-binding pocket (based onto known x-ray
data) I've forced with the overlap of some polar sidechains of the
ligand interiour with big aromatic group of the ligand itself. I've
tried resolve such clashes via energy minimization (both in the steep
and cg algorithms) but spatial overlap has not been removed. Could you
provide me with some possible ways to remove such clushes manualy?



James