|
Department of Chemistry and Chemical Biology |
Questions and problems?OPLS parametersThere 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 opls_uniX.in files of amber41, while they are described as united atoms in the uniX.in files, as well as in my old opls_uniX.in 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. Web Masters <webadmin@www.amber.ucsf.edu> Last modified: Mon Feb 5 15:50:26 PST 1996 |
|
Department of Chemistry and Chemical Biology, 102 Hurtig Hall, 360
Huntington Ave., Boston, MA 02115 Send mail to
e.chudin@neu.edu with
questions or comments about this web site.
|