normal How to assign bead types and parameters for fructose-1,6-biphosphate

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1 month 4 weeks ago #9381 by chandrimaM
Hi everyone,
Can anyone help me in assignment bead types and parameters for fructose-1,6-biphosphate?

Your help is highly appreciated.

Thanks in Advance
Chandrima Modak

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1 month 4 weeks ago #9382 by riccardo
Martini 3, I'm guessing? If so, this tutorial should get you started: cgmartini.nl/index.php/2021-martini-onli...a-new-small-molecule . I would recommend doing the tutorial first and then going through the same steps for fructose-1,6-biphosphate. We can then help you out here with fine-tuning, etc.

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1 month 3 weeks ago #9385 by chandrimaM
Hi,
I couldn't find the partition co-efficient of fructose-1,6-biphosphate. How do I proceed? I making it file what of bead types should I assign to HPO4-

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1 month 3 weeks ago #9387 by MatsMD
Hi Chandrima,

Perhaps I can comment a bit on this since you're talking about a carbohydrate and that is something Martini related I do actually know something about :-)

Part of my master's research was parameterizing carbohydrates in Martini 3, actually these parameters/mapping rules are in a pretty advanced shape and a preprint (fingers crossed!) should not be so far away.

For your problem (parameterization of the fructose-1,6-biphosphate), it would probably be a good idea to base your bead assignment/mapping on our mapping "rules" (when it is finished). We will describe recommended bead assignments, validated on partition coefficients, for common carbohydrate fragments such that lack of availability of the specific partition coefficient for your sugar shouldn't be problematic.

Hope that is a satisfactory answer, best of luck with your research!

Mats

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