[gmx-users] Atomic charges: RESP or AM1-BCC

[Oliver Schillinger]

Hi everyone,

I am trying to parametrize a ligand for use with the amber force fields 
(amber99sb-nmr1 in particular: 
https://research.chemistry.ohio-state.edu/bruschweiler/protein-force-field/).
The ligand is EGCG (http://en.wikipedia.org/wiki/Epigallocatechin_gallate).

The main focus of our studies are protein ligand interactions. Therefore 
I need to get the charges as right as possible. I computed atomic 
charges with two methods: AM1-BCC with antechamber through acpype and 
RESP at the HF/6-31G* level (according to this protocol: 
http://www.teokem.lu.se/~ulf/Methods/resp.html).

The problem:
The two sets of atomic charges are significantly different for carbons 
and oxygens, with larger absolute values for RESP (up to 2 times as 
large for some atoms).
In the validation paper for AM1-BCC 
(http://www.ncbi.nlm.nih.gov/pubmed/12395429), the AM1-BCC method 
performs slightly better than RESP when compared to HF/6-31G* ESP 
derived charges. However, when I understood it correctly, the ESP method 
is not robust and for burried atoms (methyl carbons, etc.) vastly 
varying charges can give the same quality of fit.

My Question:
Which set of charges should I use?
RESP follows the  original amber charge generation procedure more 
closely, but that does not necessarily yield more physical results of 
course.

Does anyone have a clue or experiences to share?

Kind regards,
Oliver


-- 
Oliver Schillinger
PhD student

Forschungszentrum Juelich GmbH
52425 Juelich | Germany

Building 5.8v, Room 3010
Phone: 02461-61-9532

Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt