Hyun Jung Yoon

3 Questions 1 Answers 0 Followers

Questions related from Hyun Jung Yoon

How should N-/C-termini and truncated ICL3 be treated in GPCR MD simulations using the CHARMM force field?

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...

25 April 2025 7,879 1 View

Can I use different force field for protein and ligand?

Hello, Dear! Generally, I used CHARMM36 + cgenff force field for simulaiton. But,, due to certain parts of lignad, force field cannot be generated using Cgenff. Can I use different force field...

11 July 2024 9,789 3 View

How to compare the binding pockets of two different proteins by overlapping ?

I want to compare the binding sites of two different proteins to which the same ligand binds. Alignment using residues in the binding pocket was attempted but was not effective. Are there any...

10 June 2024 3,349 1 View