normal Sucrose monolaurate - MARTINI parameters

  • zidarko
  • zidarko's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
2 months 1 week ago #7824 by zidarko
zidarko created the topic: Sucrose monolaurate - MARTINI parameters
Hi,

I want to simulate sucrose monolaurate. I have both an all-atom and a coarse grain MARTINI forcefield. For the sucrose part I used the available carbohydrate CG parameters that I modified to include a 4 bead (of type P1) tail.

Now, the issue I have now is that the molecule is supremely hydrophobic. I can for example observe the formation and disruption of aggregates at all-atom but no such thing using the coarse grain.

How do I tone down the hydrophobic character of the laurate chain?

Thanks!
Jernej

Please Log in or Create an account to join the conversation.

More
2 months 1 week ago - 2 months 1 week ago #7825 by bart
bart replied the topic: Sucrose monolaurate - MARTINI parameters
heya,

I think some things went suboptimal here. For the lauric acid part I would use the parameters you can find in the lipids download section on our webpage. You can find it here . Then the sugar I would use the default sugar model we have for sucrose, which you can find here . Now for the linker things get a bit more interesting.
Using those two as a template it will look like the following if we leave everything as is:
C1-C1-C1-P1(this P1 is the P1 from the sugar)-rest of sugar
To better represent the linker region I would move towards this:
C1-C1-N0-N0(this N0 is the old P1 of the sugar)-rest of sugar

This should give you much better results and actually represent the amphipathic nature of your molecule.
Last Edit: 2 months 1 week ago by bart. Reason: Na to n0

Please Log in or Create an account to join the conversation.

  • zidarko
  • zidarko's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
2 months 1 week ago - 2 months 1 week ago #7826 by zidarko
zidarko replied the topic: Sucrose monolaurate - MARTINI parameters
Hi Bart,

This is a great idea. Let me test it out.

It also appears I have used a bead or two too many.

Best,
Jernej
Last Edit: 2 months 1 week ago by zidarko. Reason: Added some more information.

Please Log in or Create an account to join the conversation.

Time to create page: 0.081 seconds