Quoting Donald Thomas <dthomas.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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Received on Wed Oct 26 2005 - 11:53:02 PDT
