Re: [AMBER] Capping a dipeptide with Boc

From: Alessandro Contini <alessandro.contini.unimi.it>
Date: Wed, 08 May 2019 16:33:38 +0200

Dear Saikat,
actually we used BOC, as can be seen by all images and tables, but in
the methods at p27 of the SI "acetyl" is reported instead of BOC (we
never check enough...).

Here is attached the off and frcmod files we used. By loading them into
leap you can build your peptide using BOC. For example, to build a
capped dialanine peptide, you can use the following:


loadoff BOC.off
loadamberparams BOC.frcmod
peptide = sequence {BOC ALA ALA NME}
saveamberparm peptide peptide.prmtop peptide.inpcrd
quit

Best,

Alessandro


Il 08/05/2019 14:15, Saikat Pal ha scritto:
> 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 <alessandro.contini.unimi.it> 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
> residue.
> 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.
>
> https://pubs.rsc.org/en/Content/ArticleLanding/2019/QO/C8QO01116H#!divAbstract
>
> If you want, I can send you the parameters I used as a private comunication.
>
> Best regards,
>
> Alessandro
>
>
>
> 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
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>

-- 
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
e-mail alessandro.contini.unimi.it
skype alessandrocontini
http://www.scopus.com/authid/detail.url?authorId=7003441091
http://orcid.org/0000-0002-4394-8956
http://www.researcherid.com/rid/F-5064-2012
https://loop.frontiersin.org/people/487422




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Received on Wed May 08 2019 - 08:00:02 PDT
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