Thanks Ben and Stephane
> For your molecule, with RED did you try to separate your molecule in two parts : dodecyl and charged phenylalanine ? to see if you obtain the same charges ? More which level of theory you used in your QM calculations ?
As recommended for GAFF and I used the HF/6-31G* level of theory on the entire molecule as 1 unit, in the 5 lowest energy conformations of the head group, and the nitrogen protonated giving the molecule a net +1 charge. I will split them up and redo the calculations, which should improve things.
> My question is what sort of lipid system is this? Is it a monolayer or bilayer type system that you're investigating, or some other polymer?
It is known that this surfactant probably forms micelles in solution, but the surface area per molecule is known. I will be simulating them as micelles and bilayers. My interest in this surfactant is not for biological applications so that is why it is so unusual.
Thanks
Cody
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Received on Mon Apr 15 2013 - 18:30:02 PDT
