Hello, i would like to ask about CHARMM parametrization. I am reading this paper: Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions, but no clear explanation is given. Can i modify the force field in order to recognize and treat in the way i want, interactions of some halogen atoms of drug candidate molecules and oxygen atoms of DOPC molecules. Using GROMACS and creating the lipids/drug molecule system via charmm-gui website or the charmm36-jul2022.ff.tgz force field. Thank you for your time!
Yes, you can modify CHARMM to include halogen bonding by adjusting the nonbonded parameters (electrostatic and van der Waals) for halogen atoms in your system. Use tools like CGenFF to parameterize halogen-containing drug molecules, then apply these parameters in GROMACS with the CHARMM36 force field. Ensure the interactions (halogen-oxygen) are properly treated by adjusting specific parameters in the force field files.
all of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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