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rmv Online Content
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For cyclohexane, use the new "all35_ethers" files, which includes alkanes (incl. cyclohexane).

I'd think that the carbonyl in the ring would add some strain for cyclohexanone, however.


Rick Venable
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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. frown
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 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.

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Alas, the small percentage is the case. frown

The alkanes in the ether set use the new aliphatic VDW radii, while the current lipid parameters do not. The new and improved lipid parameters, in final testing, will also use the new VDW radii. That said, the carbonyl parameters used may be more a more significant variation for the cyclic ketone. I'd probably build a couple of different cyclohexanone models, perhaps using CGenFF and "all32_lipid" sets, and compare normal mode results (VIBRAN) to each other and to expt.


Rick Venable
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At any rate, CGenFF was based upon the improved alkane VdW from the ether FF. As for the carbonyl, non of the current CHARMM force fields contains a properly parameterized ketone group. The ketone was parameterized as part of the latest carbohydrate FF, and the same parameters were transfered to CGenFF. As you say, the carbonyl parameters are probably a more significant variation. Therefore, it is advisable to use CGenFF for cyclohexanone. The only alternative would be to use the latest carbohydrate FF, but its in-ring dihedrals are highly optimized for sugars and might not be perfectly transferable to cyclic ketones.

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Thanks.. I'll probably try..

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Dear all,
Thank you so much for all your comments! Sorry, I didn't check this thread for some time) (and forget about my upper post - I didn't notice the second page of the topic when I was writing it)
I'll definitely try what you've advised and probably will bug you with further questions)

Sincerely,
Iakov

Last edited by yapolyak; 06/18/09 11:27 AM.
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So, am I right, that it would be better to create topology for cyclohexanone based on all35_ethers cyclohexane topology, but to use parameters from CGenFF? Should I than use Atom Name CG321 (aliphatic C for CH2) for the chain carbons, CG205 (carbonyl C: ketones) for carbonyl carbon and OG2D3 (carbonyl O: ketones) for the oxygen?
Or is it better to use parameters for the most molecule from all35_ethers parameter set and to take only carbonyl parameters from CGenFF?

Thanks in advance.

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I may have sown some confusion by reading "cyclohexane" instead of "cyclohexanone". This led to a discussion about the aliphatic parameters that digressed a bit from the original question. Just use CGenFF for the whole cyclohexanone molecule!

Your atom types are correct. Charge optimization is probably not required, just remove a hydrogen from acetone's methyl group and sum its charge into the carbon, then attach more carbons with standard aliphatic charges. You will be missing a CG321 CG205 bond parameter, CG321 CG205 OG2D3, CG321 CG205 CG321 and HGA2 CG321 CG205 angle parameters, and a CG2O5 CG321 CG321 OG2D3 improper, all of which can most probably be copied from acetone's respective CG331-containing parameters. Likewise, CG321 CG321 CG205 can probably be copied from the aldehyde (CG2O4 CG321 CG331). You will also be missing some dihedrals, most of which would best be parameterized by doing PES on longer linear ketones. This is actually on our to-do list, but that list is several pages long, so there's no telling when we actually get to it.

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Thanks a lot!
It seems I should read your "CHARMM General Force Field tutorial" first of all..)

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Hm, what about CG321 CG321 CG205 HGA2 improper?
Weird, but I didn't find the CG321 CG331 CG204 HGA2 improper for the aldehydes...

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