AMBER Archive (2004)

Subject: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D

From: Mikyung Seo (seo_at_ualberta.ca)
Date: Tue May 11 2004 - 17:51:01 CDT

Hello Amber members,

I am trying to calculate the charges for neutral Arg.

In Cornell et al (JACS, 1995) and Cieplak et al (J.Comp.Chem.1995),
the scheme for fitting the non-terminal amino acides was used with blocking
groups (ACE, NME).

The following are my questions according to these two articles.

1. Do I need to add two blocking groups to optimize neutral Arg using
Gaussian(6-31G*)? i.e. ACE-AA-NME in paper

2. For charge fit, the charges of C=O (C:0.5973, O:-0.5679) or N-H (N:-0.4157,
H: 0.2719) groups in the blocking groups have identical C=O and N-H charges
for adjacent residues in the protein or peptide on pg.1371, Cieplak et al
(J.Comp.Chem. 1995).

However, C=O and N-H charges are not all the above charges for all amino acids
in Cornel et al (JACS, 1995). Why do some amino acids have identical N-H and
C=O charges to the ones in blocking groups and some don't?

3. In R.E.D, can we apply specific charge constranits?
i.e. accorindg to paper, it seems to put specific C=O and N-H charges and do
charge fitting for rest atoms.

I hope my questions are not complicated.
If anybody understand how to calculate AMBER charges (Cornell et al,JACS,
1995) for amino acids, could you help me out?

Thanks in advance.
Mikyung

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