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 cyclohexan
one; I read cyclohexane. Probably I should set the font in my browser a bit larger.
If we're talking about cyclohexan
one, 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 instead.
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.