Re: [AMBER] Capping a dipeptide with Boc

From: Saikat Pal <>
Date: Wed, 8 May 2019 12:15:12 +0000 (UTC)

Thank you, sir, for your quick reply. But in this paper, you have used acetyl molecule for N terminal capping(p-S27). How to connect  C(O)-N and terminal in tleap ? 

Thanks and Regards,
Saikat Pal


    On Wednesday, 8 May, 2019, 4:45:09 pm IST, Alessandro Contini <> wrote:
 Dear Saikat,
you have to create a new residue and create specific parameters for it.
Then, you can incorporate it into the structure using tleap as any other
If you want, you can check this paper where BOC has been used to cap a
non-natural peptide, subjected to aMD and H-REMD simulations.!divAbstract

If you want, I can send you the parameters I used as a private comunication.

Best regards,


Il 08/05/2019 13:04, Saikat Pal ha scritto:
> Dear all,I want to cap a dipeptide with Boc ((CH)3C-O-(CO)-N-terminal). What is the procedure?
> Thanks and Regards,
> Saikat Pal
> _______________________________________________
> AMBER mailing list

Prof. Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 (edificio 5 ovest, III piano) 20133 Milano
tel. +390250314480
skype alessandrocontini
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Received on Wed May 08 2019 - 05:30:04 PDT
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