Roja,
Below the link to download DS Studio visualizer
http://accelrys.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php
Stéphane
----------------------------------------------------------
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 [roja.rhmn.gmail.com]
Envoyé : mercredi 9 mai 2018 19:41
À : AMBER Mailing List
Objet : Re: [AMBER] adding NME and ACE terminals
Hi,
Thank you so much dear stephane.
On Wed, 9 May 2018, 22:06 ABEL Stephane, <Stephane.ABEL.cea.fr> wrote:
> 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
>
> ----------------------------------------------------------
> 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 [roja.rhmn.gmail.com]
> Envoyé : mercredi 9 mai 2018 17:53
> À : david.case.rutgers.edu; 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
> informations?
>
> Regards
>
> On Wed, 9 May 2018, 18:54 David A Case, <david.case.rutgers.edu> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed May 09 2018 - 11:00:04 PDT
