MD simulation of a molecule with a halogen

From: Federico Rui (federico.rui_at_su.se)
Date: Wed Sep 16 2020 - 11:22:17 CDT

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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

--
Federico Riu
PhD Student
Dept. of Chemistry and Pharmacy, Sassari, Italy
Dept. of Organic Chemistry, Stockholm University, Stockholm, Sweden
federico.rui_at_su.se
friu1_at_uniss.it
+393270749349

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