[gmx-users] charges

John Kerrigan kerrigje at umdnj.edu
Tue Oct 28 14:36:02 CET 2003

Hi Anton,

Never let it be said that you overstate the obvious!  Ha! Ha!  Of course,
charges remain fixed in a molecular mechanics computation.  However, Corina
brings up a good point in regard to the methods that are used to compute
these "fixed" charges.  If you compare QM calculations of ESP charges of
different conformers of small flexible molecules, you will notice some
dramatic differences in the partial atomic charges depending upon the method
used (chelp).  The chelpg method in gaussian was developed by Breneman, et
al. to address this shortcoming.  The RESP method developed by Bayly and
Kollman was developed to address the problem of buried charges in proteins.
The GROMOS crew has opted to scale their charges to correlate with
thermodynamic properties as I understand it (please correct me).  All of
these are good methods for their respective applications.  Who knows, which
is best?  There is no established, reliable method for determining partial
atomic charge experimentally.  For the small molecules, we can use dipole
moments computed with these methods for comparison with experimental values;
however, this still does not confirm whether or not the distribution of
charge is correct.

By the way, I am a chemist by trade and education.  They gave me this
"biologist" title at the medical school so the that the MD's and
pharmacologists would not run away from me! ;)



John E. Kerrigan, Ph.D.
Computational Biologist

Adjunct Associate Professor
Dept. of Pharmacology

Academic Computing Services
RWJMS-Univ. of Medicine and Dentistry of NJ
675 Hoes Lane
Piscataway, NJ 08854

(732) 235-4473  phone
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