AMBER Archive (2005)

Subject: Re: AMBER: Using RED to calculate partial charges of new amino acid

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Oct 26 2005 - 05:36:21 CDT

Quoting Donald Thomas <dthomas_at_declan.chem.uwa.edu.au>:

> I am having a problem using RED 2 to determine the partial atomic
> charges of a new amino acid I would like to use. I'm have RED 2 working
> with Gaussian 03 or Gamess ver 27 JUN 2005 (R2) under RH Linux.
>
> My problem is actually with the procedure. The Cieplak paper in J Comp
> Chem (1995) uses Lagrange contraints to eliminate the charges on the ACE
> and NME groups of the dipeptide. The example in the RED 2 manual shows a
> very similar arrangement for ALA. But doesn't show the output.

R.E.D.-II does _not_ handle intra-molecular restraints. The tutorial available
in the RED-II manual is not for molecular fragments (central amino-acid or
nucleotide, terminal amino-acid or nucleotide), but for a 'whole' type molecule
'ACE-AA-NME' (using multi-conformation & multi-orientation RESP/ESP fit).

Deriving RESP or ESP charges for molecule fragments (i.e. for UNIT compatible
with pre-existing ones) is only performed automatically in R.E.D.-III. It
should be available beginning of 2006...

> My question is how do you tell RED about the ACE and NME groups so that
> you will be left with charges on a neutral amino acid for incorporation
> into a peptide?

For deriving RESP or ESP charges for 'AA' using ACE-AA-NME and intra-molecular
restraints:
See http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm#27

Regards, Francois

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