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charged small molecule bead mapping
- benzenekim
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1 year 1 month ago #9594
by benzenekim
charged small molecule bead mapping was created by benzenekim
Greetings :)
I'm struggling with bead mapping, on charged molecules.
In example, if I have phenolate ion, how do I map this molecule?
I think I might use Q- beads, but I don't know which Q bead(SQ5, Q3, TQ2.. etc) I have to apply.
Is there any information or guideline that helpful while choose Q-bead types?
Thank you.
I'm struggling with bead mapping, on charged molecules.
In example, if I have phenolate ion, how do I map this molecule?
I think I might use Q- beads, but I don't know which Q bead(SQ5, Q3, TQ2.. etc) I have to apply.
Is there any information or guideline that helpful while choose Q-bead types?
Thank you.
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- vainikka
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1 year 1 month ago #9596
by vainikka
Replied by vainikka on topic charged small molecule bead mapping
Hey hey,
If you haven't done so already, check out the SI of the Martini 3 paper - it contains basic rules for bead assignments and sizes.
From the top of my head I'd start with something like TQ5n - TC5 - TC5 for your molecule, but in the end it's up to you as the user to test that your models make sense.
If you haven't done so already, check out the SI of the Martini 3 paper - it contains basic rules for bead assignments and sizes.
From the top of my head I'd start with something like TQ5n - TC5 - TC5 for your molecule, but in the end it's up to you as the user to test that your models make sense.
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