Dear Gromacs users
I am trying to do energy minimisation of a protein-ligand complex. When visualising the output trajectory and .gro file, the structure of the ligand becomes distorted. The same thing happens when constraining all-bonds during EM. After running grompp, there is this note: ? In moleculetype 'zinc01509994' 12 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. ?Is this causing problems during EM, if yes then how do I add bonds/potentials/constraints in the same moleculetype? I am using Gromacs version 2016, and generated the ligand .itp/.top/.gro files using ACPYPE (the ligand conformation was obtained after docking). Regards Hershna -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
