I'm not 100% sure, but I believe
the alkane parameters in the lipid and ether force fields are identical.
I didn't notice the question was about cyclohexanone
; I read cyclohexane. Probably I should set the font in my browser a bit larger.
If we're talking about cyclohexanone
, then one should preferably use the CHARMM General Force Field (CGenFF), as Rick said. However, there are serious issues with the ketone params in the CGenFF version distributed with c36; please download the latest version
Yes, the ketone group will induce some ring strain, but probably not to an extent that would warrant introducing even more atom types and parameters. CGenFF does sacrifice some accuracy for its generality.