CHARMM Development Project Forums User Discussion & Questions Parameter Set Discussion Piperidine Parameters

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..

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

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..

The file is located in "c30a1/test/data/" or "c31a1/test/data/" this is directory location where cyclohexane.str file is.

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

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..

remember that QM data is not necessarily correct! its just another model. alex

Will they also work for cyclohexanone, or one should parameterize it by himself?

This is a fairly old post; you should be asking if new generalized small molecule FF supports cyclohexanone.

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.