Re: [AMBER] adding NME and ACE terminals

From: ABEL Stephane <>
Date: Wed, 9 May 2018 17:36:28 +0000

Hi Roja

Peptide builder can not add caps to peptides. It builds only NH3+ CCO- termini. You have to use other modeling programs such as CHIMERA, Discovery Studio Visualizer from BIOVIA* or Pymol. They are free and very useful for this particular task

* Download: Discovery Studio Visualizer

Good luck


Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
De : roja rahmani []
Envoyé : mercredi 9 mai 2018 17:53
À :; AMBER Mailing List
Objet : Re: [AMBER] adding NME and ACE terminals

I'm so sorry to ask this question here but i don't know how add terminals
in Peptide builder, would you please help me or refer me to some helpful


On Wed, 9 May 2018, 18:54 David A Case, <> wrote:

> On Wed, May 09, 2018, roja rahmani wrote:
> >
> > As i couldn't understand how build helical structure by impose command in
> > AMBER, i tried to build this structure by Peptide builder software and
> make
> > it capped in AMBER. So i want to load the .pdb file in AMBER and then add
> > NME and ACE to it.
> Use Peptide builder to make the capped peptide, then load that pdb file
> into Amber. LEaP can recognize and deal with capped ends in input pdb
> files; it is not really designed to be adding new caps to an existing,
> un-capped structure.
> ....dac
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Received on Wed May 09 2018 - 11:00:03 PDT
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