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

From: Jason Swails <>
Date: Tue, 04 Aug 2015 08:50:16 -0400

On Tue, 2015-08-04 at 20:12 +0800, lipengfei_mail wrote:
> Dear all,
> I want to construct the structure of Ala3 peptide shown as follows
> using AMBER12 package with Amber99SB force field.
> 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 does not have a template for a protonated C-terminus. You will
need to create your own if you require a protonated terminating
carboxylic acid group.

Another option is to use a neutral acetyl cap (ACE), unless you are
trying to model a tripeptide at very low pH.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 04 2015 - 06:00:03 PDT
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