AMBER Archive (2008)

Subject: AMBER: charge derivation for modified amino acids

From: Denzil Bernard (
Date: Tue Feb 26 2008 - 19:14:44 CST

I am trying to generate charges for some modified amino acids using REDII
and I had some questions regarding the application of constraints in the
resp fitting procedure.

Is it sufficient to apply the constraint to the terminal ACE and NME group
charges to zero with constraints on the amino acid residue NH and CO atoms
set to standard amber values?

When is it necessary to set the the CO and NH atoms of the ACE and NME
groups to standard amber values, and how does one do that while retaining
group neutrality.

Is the second stage of charge fitting applied to both methyl and methylene
groups or just for methyls.


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