MD simulation of a molecule with a halogen

From: Federico Rui (
Date: Wed Sep 16 2020 - 11:22:17 CDT

Dear NAMD users,

I built a molecule in CHARMM-GUI website, in Ligand Reader & Modeler section. The molecule has a bromine atom attached to a benzene, so CHARMM builds Br with a lone pair (LP1).

Using NAMD, I had problems in choosing the right amount and combination of parameter files to start the calculations. I put all the parameters I used for the other molecules, and also some CGenFF parameters from the newest version (toppar_c36_jul20).

I tried all combinations but I receive always some problems. Does anyone know what are the right parameter files to recognise a LP attached to a halogen? And there is something (parameters, force field....) I have to change in this case?

Thank you in advance


Federico Riu
PhD Student
Dept. of Chemistry and Pharmacy, Sassari, Italy
Dept. of Organic Chemistry, Stockholm University, Stockholm, Sweden

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:09 CST