AMBER Archive (2009)

Subject: Re: [AMBER] amino acids caps for truncated proteins

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Jul 16 2009 - 11:58:32 CDT

Dear Andrew,

> my question is about capping of amino acids. I would like to study
> the interaction of amyloid beta with receptors which I m studying,
> but I want to simulate only binding of the extracellular part of
> amyloid beta, but not the transmembrane part. How is it possible to
> make cap to C-tail/N-tails of proteins in Amber and which cap is
> better to use?

You could keep the protein domain you are interested in and put at the
N-terminal side the MeCO residue (ACE) and at the C-terminal side the
NHMe residue (NME).

To make the caps, remove the residues you are not interested in from
your PDB structure; leaving only the carbonyl carbon of the 1st
residue, and the amide nitrogen of last residue to be kept. Rename the
residue name of this carbonyl carbon into ACE and the residue name of
this amide nitrogen into NME. Load your structure in LEaP. LEaP should
add the missing atoms for the ACE and NME residue.

regards, Francois

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