CCL: Obtaining a compilation of OPLS-AA force field parameters


Hi Andrew.Â

There have a couple of additions that I know of. One involved a biological fragment and the other was incorporating the "sigma hole" phenomenon. There are also OPLS-AA parameters which have been produced by Acevedo regarding ionic liquids, and a few which I've created. At least, I'm sure that my all-atom methanol, which drastically increased the accuracy of a substitution reaction over united-atom methanol, hasn't been published.Â

In any case, you'll want to use the parameters which are included with BOSS, so TINKER's parameters would be ideal. Check out the papers that Jorgensen's published laterly. I follow his work fairly closely. That one biological fragment may be relevant to you, as might the sigma hole.

But I've met Jorgensen and know a couple of people in his group. They're all really nice. Shoot Bill an email requesting the latest compilation.Â


Regards,
BW




--
Billy Wayne McCann, Ph.D.
irc://irc.freenode.net:bwayne
 "A rich man will always desire what his wealth cannot acquire." ~ Faust (Goethe)



On Sun, Aug 24, 2014 at 9:09 PM, Andrew DeYoung andrewdaviddeyoung[*]gmail.com <owner-chemistry{=}ccl.net> wrote:
Hi,

Does anyone know where I can obtain a compilation of OPLS-AA force field parameters?

The OPLS-AA force field has been developed over many years by the Jorgensen Group at Yale. ÂThe parameters have been developed and disseminated in many publications over the years. ÂI am wondering if there is a compiled list of all the OPLS-AA parameters. ÂI thought that perhaps the Jorgensen Group website ( http://zarbi.chem.yale.edu/index.html ) might have such a compilation, but I can't seem to find one there.

I'm a user of the GROMACS MD package ( http://www.gromacs.org/ ). ÂGROMACS contains library force field files ( usually located in /usr/local/gromacs/share/gromacs/top ), including ones for OPLS-AA. ÂBut I'm not sure if these are "official" compilations. ÂThere are a lot of comments sprinkled throughout these files, including several that seem to indicate a variety of revisions.

Another possible list of parameters is found at the TINKER website:

http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm

The heading of that file includes this comment:

"The parameters supplied with TINKER are from "OPLS All-Atom Parameters for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as provided by W. L. Jorgensen, Yale University during June 2009. These parameters are taken from those distributed with BOSS Version 4.8."

So, that list appears to be fairly recent (July 2008 and June 2009). ÂI don't know if there have been many changes/additions to OPLS-AA in the last few years; browsing through the literature, it seems perhaps not. ÂBut, nevertheless, does anyone know where I can obtain a fairly recent and official compilation of the OPLS-AA force field parameters? Â

Thank you so very much for your time!

Andrew DeYoung
Carnegie Mellon University