normal Tutorial on Sugars

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5 years 7 months ago #3492 by robrob2013
Tutorial on Sugars was created by robrob2013
Hi I am planning to simulate a lipid bilayer covered by MALTOHEPTAOSE (AMylose)

However, I dont know how I could produce a CG gro file of MALTOHEPTAOSE.
I have already checked the extension file of sugars (martini_v2.0_sugars.itp)
but still I'm clueless on how to start with this.

is there a tutorial that deals with the basics of dealing something like this?

Thank you everyone!

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5 years 7 months ago - 5 years 7 months ago #3493 by Clement
Replied by Clement on topic Tutorial on Sugars
Hi Rob,

Nope, sadly we do not have such tutorial. At least not on sugar specifically. But by comparing the AA structure of your molecule and how the CG models are derived from simpler sugars, you can come up with something. If my eyes serve, I'd say your maltoheptaose is just a polymer of seven glucose molecules; you can check and compare to the maltose structure (polymer of two glucose molecules) in the sugar .itp file to have an idea of how to build a more complex sugar...

Do not hesitate to post intermediary steps here...

Good luck!
Last edit: 5 years 7 months ago by Clement.

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5 years 7 months ago #3498 by siewert
Replied by siewert on topic Tutorial on Sugars
Maltose is present in the itp file, so that couldn't be the problem.

Generating a starting gro file is easy - putting the right amount of constituting CG beads randomly in a box could already serve as a suitable starting coordinates file, as Martini molecules are very easily energy minimized.

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