Re: AMBER: Atomic charges and internal H-bond

From: Jiri Sponer <>
Date: Tue, 7 Oct 2003 16:12:27 +0200 (MEST)

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> Dear AMBER community,
> I am calculating partial charges on organic fragments via HF/6-31G* optimization and ESP and RESP fit. In some structures, there are internal H-bonds and the fit yields more negative charges on atoms involved in the H-bond than I expect (e.g.donor nitrogen -0.6).
> Is this an artifact of the fit or does it reflect the electrostatic behavior of the H-bond? How shall I go on when I want to have this internal H-bond during dynamics?
> For other structures, I optimized with dihedral restraints to avoid internal H-bonds. What cutoff for donor hydrogen-acceptor distance should be used so that the fit wouldn't be much influenced? Is there a study on the effect of the H-bonds on the quality of ESP fit?
> Thank you in advance for your responses.
> Regards,
> Martin Lepsik

Partial charges, in general, have no quantum mechanical operator.
Thus they do not represent any observable physchem quantity,
in reality they do not exist.
Thus, all charge distributions are arbitrary.
In case of ESP charges it is important that all of them taken together
reproduce the ESP (ESP has a QM operator). Irrespective
of the values of the INDIVIDUAL charges.
   If you think this charge is too negative you can possibly restrain/constrain
   it and the remaining charges would be adjusted accordingly
   to reproduce the ESP.

   Best wishes Jiri

Jiri Sponer
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
fax: 420 5412 12179
phone: 420 5415 17133
Senior Wellcome Trust International Research Fellow for Biomedical Science

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Received on Tue Oct 07 2003 - 15:53:01 PDT
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