AMBER Archive (2009)

Subject: Re: [AMBER] query about the charge fitting procedure about C- and N-terminal residues

From: FyD (
Date: Fri Jun 26 2009 - 04:41:52 CDT

Dear Ye Mei,

> Recently, I noticed that the atomic charges of N-terminal residues differ
> a lot between ff94 and ff03. In ff03 paper, I only found explanation for
> the fitting procedure for non-terminal residues. So I am wondering how
> the atomic charges were fitted for C- and N-terminal residues. Can
> anyone tell me?

I think terminal fragments are not present in the Duan et al. FF
because they are considered exposed to the solvent. Consequently,
these from the Cornell et al. FF are used instead.

Please see:
P. Cieplak, W.D. Cornell, C. Bayly & P.A. Kollman, Application of the
multimolecule and multiconformational RESP methodology to biopolymers:
Charge derivation for DNA, RNA, and proteins. J. Comput. Chem. 1995,
16, 1357-1377.
   & tutorials @:

regards, Francois

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