Questions and problems?

OPLS parameters

There is something in the OPLS database input that I find strange: Residues HID, HIE, HIP, TRP, PHE and TYR are described with "ALL ATOM AROMATIC PARAMETERS" in the files of amber41, while they are described as united atoms in the files, as well as in my old files of amber4.

OPLS is now a "mixed" force field, where aliphatic CH, CH2 and CH3 groups are united atoms, and everything else (including aromatic CH groups) is all atom. So the "uni" is not quite correct.

Also, I believe people should be *dis*couraged from using residues like TYU, except for the purpose of reproducing old data, or for other places where the inaccuracies of that force field are not important. It was problems with the united atom aromatics that led Jorgensen's group to make them all-atom.