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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
