Chih-Ying Lin wrote:
Hi
Honestly, I don't know how to do the quantum chemistry calculation.
I have the one azobenzene derivative force field parameters(from QM/MM
paper) in hand.
This azobenzene derivative is quite similar with the azotab compound,
which I need.
For the rest parts of the azotab compound I try to used the default
force field parameters, which come from either Amber or Gromacs
package.
Will it be reasonable to determine the force field parameters of the
new compound like I mentioned above?
Azotab will put into water; however, the force field parameters of the
azobenzene derivative are coming from the QM/MM calculation in gas
phase. So, will it be wrong afterall?
The general answer to this type of question is that you have to derive
the parameters for a compound in a way that is compatible with the force
field you choose to use. For an AMBER-type force field, quantum
calculations may be in order. For a FF like OPLS and GROMOS, empirical
derivation/adjustment and free energy calculations are the correct protocol.
Bottom line: read that paper regarding the derivation of the force field
you want, and follow that methodology.
-Justin
Thanks a lot
Lin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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