Hi everyone,

I am planning to perform MD simulations on a GPCR that contains an unstructured ICL3 region (~70 amino acids). I would like to ask for advice regarding N- and C-terminal treatment in this context.

  • For a typical GPCR protein, is it more appropriate to apply NTER and CTER patches, or should I use ACE and CT3 (NME) caps instead, especially when using the CHARMM36 force field?
  • If I decide to remove the ICL3 loop entirely prior to simulation, what would be the best practice for treating the break points at the junctions? Should I cap the residues in any specific way to avoid artifacts due to dangling termini or unnatural charges?
  • Any insights or references related to CHARMM force field conventions or best practices in GPCR modeling would be greatly appreciated.

    Thank you!

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