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Cholesteryl oleate parameters
#37859 04/30/20 08:39 PM
Joined: Apr 2020
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J
JayB Offline OP
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Hello all,

I have a question regarding the parametrization of the molecule cholesteryl oleate. I have not been able to find this molecule anywhere in the CHARMM documents, but I realize that there are parameters for cholesterol and oleic acid respectively. I just need to find a way to connect them together. I need parameters for the region that links the cholesterol to the oleate chain.
This process is new to me, and after reading around it seems that there a couple routes to go down:

1) I am aware of CGenFF as a method to do parametrization, however it is noted that biological macromolecules such as lipids are already optimized, so this option seems off the table.
2) Borrow parameters from similar structures: This method was used in a previous paper that created a cholesteryl ester in the CHARMM forcefield, however we are worried this technique is not sufficient or accurate. Would this work?
3) Do QM calculations for the linkage of the two molecules.

What is the best way to go about this? Any guidance would be helpful.

Thank you

Re: Cholesteryl oleate parameters
JayB #37860 05/01/20 12:34 AM
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rmv Offline
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The preferred approach is to use CGenFF on a small fragment that represents the linkage, and then define a new residue where only the linkage uses any of the newly derived parameters, with the existing FF used as much as possible. The QM may be needed if the penalties are large, but may not be needed for this case.


Rick Venable
computational chemist


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