4) Since cholesterol has different atom types how should I put it in the cgenff files.
Actually, there's a cholesterol topology in CGenFF as well so you can represent your entire molecule with CGenFF.
I would recommend doing a full parameterization - charges, equilibrium geometry, vibrations and potential energy scan - on butenone, (or, for even better accuracy and transferability, cis and trans 3-penten-2-one, as suggested by rmv). Must-reads before doing this are:
- The CGenFF paper
- The CGenFF tutorial
- The CGenFF FAQ
- Poker's molvib tutorial
- Threads by various people on this forum who have successfully parameterized molecules
An experienced CGenFF worker can get through the whole parameterization procedure in one or two days. However, the first time usually takes much longer, about two weeks on average. And that's for people working in our group; if your only source of support is this forum, it may easily take you 3 or 4 weeks. I'm telling you this because the enone moiety is actually on the to-do list of a grad student in our lab. It's very difficult for me to estimate when she will be done with it because my boss can give her a different and urgent assignment any time, but if nothing goes wrong, she might be finished with it by the beginning of December. So you have the choice between committing a few weeks to this parameterization and be reasonably sure to have your parameters somewhere mid or end November, or gambling that everything will work out well at our end and that you will get the parameters from us by mid-December (but I have to stress again that I can make no guarantees whatsoever).