AMBER Archive (2004)

Subject: Re: AMBER: Some questions in building a new residue

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Mar 10 2004 - 14:31:25 CST

Dear Chung-Chien Wei,

As said Ilyas Yildirim, it is very unlikely you will be able to reproduce the
published charge values. It is obviously true that for a same molecule,
different conformations can be selected and then different sets of ESP/RESP
charges produced. A more tricky problem is that even for a SAME optimized
conformation, the molecular orientation also affects charge values... (And I do
not talk about the optimization thresholds used by the ab-initio software that
can induce also charge differences...) Even for small molecules like EtOH, DMSO
or DMP (which seems to be very simple cases for deriving RESP charges) the
charge differences obtained can be highly disturbing and tricky...

Now concerning the charge differences you reported (in comparison to the work of
Duan et al.), in my opinion, you have errors in your inputs (the differences are
too big!). To learn how to derive RESP charges, a very good starting point is
the work of Cieplak et al. in J. Comput. Chem. 1995, 16, 1357-1377. We also
wrote the program RED http://www.u-picardie.fr/labo/lbpd/RED/ to help people to
derive RESP charges. A multi-orientation RESP/ESP fit can be automatically
performed (by analogy to the multi-orientation RESP fit). The new version of RED
will incorporate automatic multi-orientation, multi-conformation and extra-point
handling...

In the Cieplak et al. paper, there are details about how to use blocking groups
(NMe & ACE, as you are interested in...) in the RESP charge derivation and more
generally how to use multi-conformational RESP fit with or without charge group
restraints.

Regards, Francois

F.-Y. Dupradeau
 --
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
 --
http://www.u-picardie.fr/labo/lbpd/fyd.htm
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