AMBER Archive (2006)

Subject: Re: AMBER: Charges of enantiomers for Amber8

From: FyD (fyd_at_u-picardie.fr)
Date: Thu Jan 26 2006 - 01:53:43 CST

Quoting lily ferreira <lily_1_mart_at_yahoo.fr>:

> Fitting is not averaging! But at the end of the RESP
> calculations do we have to average the 10 charges?

Please, read the R.E.D.-II manual & tutorial, and you will get it...

In short, you can use one conf. to generate the charges for your molecule (1 set
of charge values) in a _single_ RESP run
or
N conf. to generate the charges for your molecule [1 (but different) set of
charge values] again in a _single_ RESP run.

The single set of charges has to "represent" the different conformations (and
orientations) of your structure...

> Because when we use LEaP,
> we have only to work with one set of charges for the enantiomers! So, how
> to procede after the calculation of the RESP charges of our 10
> conformations?

The set of charge values generated is generally independent of the mol.
orientation, mol. conformation and chirality (enantio. and even diastero.
althought more strange for me). LEaP recognizes a 'structure' based on
atom/residue names found in the OFF library and then just use the charges/FF
atom types corresponding to the atom names defined in this OFF file.

regards, Francois

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