FATAL ERROR: FOUND ISOLATED LONE PAIR

From: Nibedita Ray Chaudhuri (nivirc.143_at_gmail.com)
Date: Fri Nov 01 2019 - 07:35:49 CDT

Hello,
I am trying to simulate a protein-ligand complex where the ligand consists
of halogens. As you know the latest CGenff version describes halogen bonds
with lone pairs (http://doi.org/10.1016/j.bmc.2016.06.034), I am dealing
the same but got stuck while running the system on NAMD. I have tried with
version 2.13, but getting the following error :
FATAL ERROR: FOUND ISOLATED LONE PAIR PARTICLE 5109

I have followed some previous post on the matter but not quite sure whether
NAMD can deal with lone pairs or not. So, any suggestion would be
appreciated.
Thank you.

Nibedita Ray Chaudhuri
Research Fellow
Division of Bioinformatics
Bose Institute (Centenary Campus)
India

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