Assigning partial charges in topology file

From: Christian Jorgensen (
Date: Thu Oct 14 2010 - 13:57:30 CDT

I am trying to build the local topolgy file for a ligand that we are studying. I tried to do this from the standard topology file top_all27_prot_lipid.inp, howeve by comparing the structure of my ligand to analogous amino acids, however the partial charges for the same atom types vary depending on what residue I consider.

e.g. in HSE: ATOM CB CT2 -0.18
e.g. in HSD: ATOM CB CT2 -0.09
e.g. in HSP: ATOM CB CT2 -0.05

This means I cannot guess what charges to assign to the atom groups.
Any help as to how to do this? My approach has been to find the amino acid that most closely resembles my structure and work from there, does that seem reasonable?

I realise there are sophisticated QM methods to partition partial charges, but I would want to avoid this if possible as the ligand I am studying is structurally very simple.

Regards, Christian

Merton College, Oxford / PTCL

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