Re: [AMBER] How to construct the Ala3 peptide shown in this picture?

From: David A Case <>
Date: Tue, 4 Aug 2015 09:06:35 -0400

On Tue, Aug 04, 2015, lipengfei_mail wrote:

> I have tried to use the sequence {NALA ALA CALA } in the tleap, but I failed.
> Because I must keep the N-terminus of the peptide be protonated, the
> C-terminus be neutralized.

Amber doesn't have libraries for protonated C-terminal residues. You will
have to build your own, probably using tutorial B5 as an introduction to
creating library files for modified amino acids.

(Maybe someone in the constant pH business has input that could help here...)


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Received on Tue Aug 04 2015 - 06:30:02 PDT
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