AMBER Archive (2007)

Subject: AMBER: Non-standard amino acid residue

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Mon Jul 16 2007 - 09:44:32 CDT

Dear AMBER users,

I'm trying to introduce non-standard amino acid residue into my protein
for the further MD simulation. To accomplish that I get the parameters
for -NH-CHR-CO- in ANTECHAMBER. Then I create the library for the
residue and add it into the libraries in Xleap and so on. I realized
that the charges for N, C, CA (and the other, of course, too) atoms in
the prepin file are quite different (for a example for peptide bonded N
with the calculated n1 type it is at least 0.2-0.3 charge units more
negative than peptide bonded N in standard amino acid ) compared to
standard amino acids. It is not a surprise since 1. AM1-BCC method for
sure should give the results different from standard AMBER charges 2. N
atom, for example, has one more uncoupled electron pair compared to the
N atom in peptide-bonded state. Is there the way to use non-standard
amino acid residues within the protein without this charge problem?

Thank you very much in advance for the answer!

Sergey
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