Nancy wrote:
Hello,
I have successfully minimised and equilibrated two systems, one
consisting of a single molecule of ethylene glycol (1,2-ethanediol) in a
water box, and the other is one molecule of glycerol, also in a water
box. I am planning to proceed to simulate other sugar alcohols (e.g.
erythritol, arabitol, mannitol, etc). I used topolbuild 1.2 to generate
topologies for ethanediol and glycerol, and for the various atoms in
these molecules, I used charge values from methanol (the methanol
tutorial included with GROMACS), i.e. +0.398 for hydroxyl hydrogens,
-0.574 for oxygens, and +0.176 for the carbons.
As I told you before, the origin of these charges, in the absence of some
published validation of the parameters, is questionable at best.
Should I use these charge values for an arbitrary sugar alcohol, or
should I use the charge values specified in the article:
"OPLS All-Atom Force Field for Carbohydrates". Damm, W., A. Frontera, J.
Tirado-Rives, and W. L. Jorgensen. 1997. J. Comput. Chem. 18:1955–1970.
If you are using OPLS, probably yes. But as I recall, you were running
simulations with GROMOS96. If this is the case, then using OPLS charges or
other parameters is wholly inappropriate. The simple fact is, you must use
charges from the parameter set you intend to simulate, otherwise go through the
laborious process of deriving them yourself.
Also, are there programs that will automatically generate charge values
and other parameters for an arbitrary molecule?
There are several options, like the R.E.D. server or antechamber (available from
the Amber folks), but be advised that you should always follow the methodology
for whatever force field you're using. If it's GROMOS (like you've been using
before), neither of these approaches is necessary, and they may not give you
correct parameters. Read the primary literature and base your decisions on what
you find.
-Justin
Thank you.
Nancy
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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