[gmx-users] Carboxylate OPLS-AA parameters
jalemkul at vt.edu
Sun Jan 26 03:25:33 CET 2014
On 1/25/14, 9:10 PM, rankinb wrote:
> I am now thoroughly confused. I have read papers that report the OPLS-AA
> sigma and epsilon values, as well as atom charges. The latter charges match
> those in the ffoplsaanb.itp file. I am not doing any fancy simulations and
> only want to compare basic information between simulations of butanoic acid
> and butanoate. I already have the topology file for butanoic acid and just
> want to determine the change in the number of water molecules in the first
> coordination shell when going from a neutral to negatively charged molecule.
I suppose I should have been a bit more specific. The charges in
ffnonbonded.itp are not used for anything *in Gromacs* and so they really aren't
useful, though they do, of course, line up with published values if you want to
go to the trouble of parsing through tables of hundreds of atom types ;)
The best and most convenient reference for implementation is aminoacids.rtp.
There, you will find, for instance ASP/ASPH and GLU/GLUH. These are the ionized
and neutral forms of the acidic amino acids, bearing charges that you can use
for your molecules. Standard practice in OPLS-AA is that all aliphatic H atoms
have a +0.06 charge, and the central carbon to which they are bound has an equal
negative charge to balance the hydrogens, i.e. -0.18 for a C in CH3, -0.12 for C
in CH2. From that, you can easily piece together reasonable topologies for your
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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