AMBER Archive (2009)

Subject: [AMBER] amino acids caps for truncated proteins

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Thu Jul 16 2009 - 11:31:18 CDT

Dear Amber users,
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?

Best regards,
Andrew Voronkov

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