[gmx-users] OPLS-FF

If I understand correctly, the rebuilt residues do not connect to each side of the gap correctly? You state about gaps: "actually it shouldn't appear after minimisation.", but it is not necessarily true that EM is capable of bringing the residues properly close together. I think you mean th

[gmx-users] OPLS-FF

Hi all, My protein contain some missing residues , so I rebuilt missing residues, although gap is there between helices, my idea is when do minimisation these gap should disappear. Later trying to use pdb2gmx with OPLS/aa-L FF for generating gro file for two systems containing protonated and anothe