unanswered Fine tuning of an "active site"

  • denniqo
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8 months 6 days ago #9693 by denniqo
Fine tuning of an "active site" was created by denniqo
Hey guys i didn't know where to ask this, but i hope this forum is fitting. So i am doing coarse-grained simulation with an potassium ion channel and they work pretty fine, except that the negative charge distribution of the pore is not very well conserved in the cg martini simulations. Cl- ions can enter the pore together with the Na+ ions (same bead type as potassium). The pore consists of backbone oxygens and in all-atomic simulations these carry a partial charge of -0.51 and create a very negative pore. In the CG Martini representation the BB beads of the residues forming the pore are typically SP1-2/P2. I tried to add an a label to them, which didn't hinder the Cl- ions to enter the pore. Does anyone have any experience with fine tuning a protein using the new labels in martini 3? Should i give the backbone beads a partial negative charge with the q label? Should i change the bead type to a more polar bead type in general? There i so many things one could try that i don't really now where to start.

Thank you :)

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