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

From: lipengfei_mail <lipengfei_mail.126.com>
Date: Tue, 4 Aug 2015 20:12:38 +0800 (CST)

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.



How do I get it?
Please help me in this regard in brief.
Thank you very much !

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Pengfei Li
Email:lipengfei_mail.126.com







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Ala3.png
(image/png attachment: Ala3.png)

Received on Tue Aug 04 2015 - 05:30:03 PDT
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