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

[Alan]

Dear Oliver, I’d recommend to try http://q4md-forcefieldtools.org/REDS/. If
you did all right, it should  t least confirm your RESP results.

Alan


On 19 May 2014 07:20, Oliver Schillinger <o.schillinger at fz-juelich.de>wrote:

> 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
>
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> 52425 Juelich | Germany
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-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588