[gmx-users] Preparation protein-ligand complex

[Felipe Pineda, PhD]

https://mcule.com/apps/1-click-docking/

On 03/01/2013 11:03 AM, James Starlight wrote:
> 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