Re: [AMBER] NPA charge for the ligand

From: FyD <>
Date: Mon, 15 Oct 2012 10:37:11 +0200

Dear Mu Xia,

As you know Amber force fields (FF) are strongly connected to the RESP
charge model and to AM1-BCC charges. AM1-BCC has been developed to
correctly reproduce molecular electrostatic potentials (MEP) computed
by quantum mechanics, providing a fast approach for deriving MEP based
charge values. However, the computational cost of RESP charges is
nowadays close to zero considering the increase of computer power and
the availability of new tools such as R.E.D. Server.

Originally the RESP charge model has been developed to overcome
limitations of charge values calculated using other models such as
population analyses (Mulliken or Lwdin population analysis). However,
Antechamber has incorporated many different charge models adding I
think ambiguity to charge derivation for Amber FF, but allowing also
users to make their own choices.

Thus, my feeling is that you can use natural population analysis or
even the charge model of your choice in whatever FF if you rigorously
validate/demonstrate that this 'works'. Obviously, using the RESP
charge model for Amber seems more 'natural'...

I hope this helps.

regards, Francois

> I noticed that we can use RESP and AM1-BCC methods to calculate the
> charge distribution of the ligand while running MD.
> My question is: can I use the NPA charge model in order to
> calculate the atomic point charges of the ligand?

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Received on Mon Oct 15 2012 - 02:00:03 PDT
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