[gmx-users] query on OPLS-2005

[Sanku M]

Hi Cara,
   Thanks for a  very clarifying email. It helps a lot.
Sanku


________________________________
From: Cara Kreck <cara_a_k at hotmail.com>
To: gmx-users at gromacs.org
Sent: Friday, October 28, 2011 3:50 AM
Subject: RE: [gmx-users] query on OPLS-2005


 
 
Hi Sanku

According to the Schrodinger Knowledge Base, this is the paper that should be referenced for OPLS-2005 instead:
Banks, J.L., H.S. Beard, Y. Cao, A.E. Cho, W. Damm, R. Farid, A.K. Felts,T.A. Halgren, D.T. Mainz, J.R. Maple, R. Murphy, D.M. Philipp, M.P. Repasky,L.Y. Zhang, B.J. Berne, R.A. Friesner, E. Gallicchio, and R.M. Levy. Integrated Modeling Program, Applied Chemical Theory (IMPACT). J. Comp. Chem., 26, 1752 (2005)
(http://onlinelibrary.wiley.com/doi/10.1002/jcc.20292/full)

The Gromacs oplsaa.ff/forcefield.doc file says OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

OPLS-AA/L seems to presented in the above paper as their updated version, but it is sourced from the 2001 paper on proteins which is listed as a reference in the Gromacs oplsaa.ff/forcefield.itp file. The 2005 paper then adds  the following:
"New force-field parameters were developed for OPLS_2003 for organic 
functional groups for which the OPLS_2001 force field does not provide 
specific parameters. Previously derived parameters for proteins, discussed above, were implemented without modification in OPLS_2003." (Where 2003 apparently evolved into 2005).

So it looks like the protein section of both force-fields are the same, but if you want to use other parameters you should check them individually first to see whether or not they were changed or created since 2001.

Cara





________________________________
Date: Wed, 26 Oct 2011 15:02:07 -0700
From: msanku65 at yahoo.com
To: gmx-users at gromacs.org
Subject: [gmx-users] query on OPLS-2005


Hi,
  I wanted to check what is actually OPLS-2005 forcefield that is recently being referred often for md simulation. However, I also see that whenever, OPLS-2005 is being referred, it cites a 2001 paper by Jorgensen on OPLS forcefield. So, what is actually OPLS-2005?
So, I wonder what version of OPLS forcefield is present in gromacs 4.5 series. Is it also so-called OPLS-2005 forcefield?
Sanku
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