AMBER Archive (2005)

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

From: Donald Thomas (dthomas_at_declan.chem.uwa.edu.au)
Date: Tue Oct 25 2005 - 09:50:40 CDT

Hi All,

  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.

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?

Thanks, 

-- 
Donald Thomas <d.thomas_at_usask.ca>
University of Saskatchewan

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