CHARMM Development Project
Posted By: Baloo Piperidine Parameters - 01/17/05 09:19 AM
Dear All,

Has anyone come across the bond length, bond angle, torsion angle and phase values of Piperidine or Cyclohexane. Please guide me for the same.

Can these values be picked from the Proline parameters. I know that the piperidine or cyclohexane is not a planar structure.

Best Wishes..
Posted By: preeti Re: Piperidine Parameters - 01/19/05 03:21 AM
Hello,

For cyclohexane, look into test/data/cyclohexane.str file available.

Dpending upon what conformation of cycloheaxne you want, try looking into , pickett and strauss paper in JACS or Stefan Fischer's (Harvard university) thesis or Fischer/Prof. Karplus papers. You can get all the information.

Hope this helps!
preeti
Posted By: Baloo Re: Piperidine Parameters - 01/19/05 09:12 AM
Hi Preeti,

Thanks for providing information. However could you please tell me where I will find cyclohexane.str file. As I donot find file with this name in /test/data directory

Best Wishes..
Posted By: preeti Re: Piperidine Parameters - 01/19/05 04:58 PM
The file is located in "c30a1/test/data/" or "c31a1/test/data/" this is directory location where cyclohexane.str file is.
Posted By: alex Re: Piperidine Parameters - 01/25/05 12:28 PM
note that the standard charmm protein parameters will treat cyclohexane. you just need to create the residue in the topology file. piperdine will require some actual parameter development.

alex
Posted By: Baloo Re: Piperidine Parameters - 01/27/05 11:36 AM
i have measured the parameters for the cyclohexane after doing QM calculation and they donot match with standard charmm protein parameters. So i think one has to create and new atom type and assign the new values of parameters to that atom types for cyclohexane. The same holds true for piperidine.

best wishes..
Posted By: alex Re: Piperidine Parameters - 02/10/05 01:01 PM
remember that QM data is not necessarily correct! its just another model. alex
Posted By: yapolyak Re: Piperidine Parameters - 06/02/09 04:09 PM
Will they also work for cyclohexanone, or one should parameterize it by himself?
Posted By: rmv Re: Piperidine Parameters - 06/02/09 04:54 PM
This is a fairly old post; you should be asking if new generalized small molecule FF supports cyclohexanone.
Posted By: Kenno Re: Piperidine Parameters - 06/02/09 06:03 PM
As there isn't a lot of ring strain in cyclohexane, the general force field represents it with plain aliphatic carbon types and charges. You could probably make a cyclohexane model using atom types and parameters from the lipid FF and get very similar results.
Posted By: rmv Re: Piperidine Parameters - 06/02/09 07:56 PM
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.
Posted By: Kenno Re: Piperidine Parameters - 06/02/09 10:06 PM
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.
Posted By: rmv Re: Piperidine Parameters - 06/02/09 10:32 PM
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.
Posted By: Kenno Re: Piperidine Parameters - 06/03/09 02:56 PM
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.
Posted By: yapolyak Re: Piperidine Parameters - 06/18/09 11:13 AM
Thanks.. I'll probably try..
Posted By: yapolyak Re: Piperidine Parameters - 06/18/09 11:25 AM
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
Posted By: yapolyak Re: Piperidine Parameters - 06/19/09 02:32 PM
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.
Posted By: Kenno Re: Piperidine Parameters - 06/19/09 03:18 PM
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.
Posted By: yapolyak Re: Piperidine Parameters - 06/19/09 04:12 PM
Thanks a lot!
It seems I should read your "CHARMM General Force Field tutorial" first of all..)
Posted By: yapolyak Re: Piperidine Parameters - 06/19/09 05:58 PM
Hm, what about CG321 CG321 CG205 HGA2 improper?
Weird, but I didn't find the CG321 CG331 CG204 HGA2 improper for the aldehydes...
Posted By: yapolyak Re: Piperidine Parameters - 06/19/09 06:06 PM
Also, what if to take some of the dihedrals from all35_ethers FF?
Or it would be too inaccurate?
Posted By: yapolyak Re: Piperidine Parameters - 06/19/09 06:08 PM
The crystal structure of cyclohexanone also has a chair conformation - may be oxygen doesn't imply that big constrains...
Posted By: Kenno Re: Piperidine Parameters - 06/22/09 07:51 PM
Originally Posted By: yapolyak
Hm, what about CG321 CG321 CG205 HGA2 improper?
Weird, but I didn't find the CG321 CG331 CG204 HGA2 improper for the aldehydes...

Do not introduce impropers for sp3 centers! eek Not even all sp2 centers have impropers in CHARMM. You should have exactly 1 improper parameter in cyclohexanone, which should be explicitly defined both in the topology and in the parameter.

Make sure you thoroughly understand the meaning of the different terms in the force field's potential energy function. Additionally, it wouldn't hurt to read some of Alex MacKerell's force field papers to make yourself familiar with CHARMM's parameterization philosophy.

Originally Posted By: yapolyak
Also, what if to take some of the dihedrals from all35_ethers FF?

We did that already when building CGenFF. As a result, Alex and I together spent many weeks if not months eliminating side-effects. You see, in force field parameterization, dihedral parameters typically are the final term optimized, thereby accounting for the contribution of long range non-bond interactions to the PES. In this light, you may understand that you're just asking for errors in your force field. And good luck explaining to your papers' reviewers why you chose to play mix-and-match with force fields whilst having a force field at your disposal that has all the parameters you need and is expressly designed for the class of molecules you're studying...

What you could do is copy the "outer" dihedral parameters from other general force field molecules. Specifically, CG2O5 CG321 CG321 CG321 and CG2O5 CG321 CG321 HGA2 can respectively be copied from the ester's CG2O2 CG321 CG321 CG321 and CG2O2 CG321 CG321 HGA2. It's not ideal, but it may do. You will probably even get away with copying CG321 CG2O5 CG321 HGA2 and OG2D3 CG2O5 CG321 HGA2 from acetone's CG331 CG2O5 CG331 HGA3 and OG2D3 CG2O5 CG331 HGA3. But you can hardly escape doing a potential energy scan on butanone for CG321 CG2O5 CG321 CG321 and OG2D3 CG2O5 CG321 CG321 ! This is actually not a bad deal. You don't need to optimize any charges, bonds, angles or impropers; all you have to do is one potential energy scan on a very simple model compound. Following the procedure and the example scripts in the tutorial, this should really be a breeze. If you want, I can even take a look at your toppar file once you're finished.
Posted By: yapolyak Re: Piperidine Parameters - 06/24/09 12:51 PM
Quote:
Do not introduce impropers for sp3 centers!

Ups...) Yep, I definitely should read more background papers)

I see.. Thank you very much! I'll go through your manual and will try to finish my toppar file appropriately (and show it to you if you don't mind grin )

Sincerely,
Iakov
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