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How to assign bead types and parameters for fructose-1,6-biphosphate
- chandrimaM
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1 year 11 months ago #9381
by chandrimaM
How to assign bead types and parameters for fructose-1,6-biphosphate was created 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
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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- riccardo
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1 year 11 months ago #9382
by riccardo
Replied by riccardo on topic How to assign bead types and parameters for fructose-1,6-biphosphate
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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- chandrimaM
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1 year 11 months ago #9385
by chandrimaM
Replied by chandrimaM on topic How to assign bead types and parameters for fructose-1,6-biphosphate
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-
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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- MatsMD
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1 year 11 months ago #9387
by MatsMD
Replied by MatsMD on topic How to assign bead types and parameters for fructose-1,6-biphosphate
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
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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