Hi,
As Carlos said the AMBER suite has all the tools you need to constructed a given peptide according to the Amber nomenclature (atom orders and names in the peptide sequence). If you do not how to use them you have to read the manual. You do not want to read it you could use the tools I suggested and use pdb2gmx.
Also not that with ProBuilder you can choose the output format of the PDB
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 : lundi 7 mai 2018 12:19
À : AMBER Mailing List
Objet : Re: [AMBER] Poly amino acid helix form topology files
Because i want topology file which is compatible with AMBER99 ff in GROMACS.
I can make the simple THR sequences just in order and its topology file
with tleap,parmed,.. but i want its capped helical structure and it is so
different in parameter,... as you know. Because of that i asked here to
know if it is possible to make this structure directly in ambertools to be
more trusted and compatible in next step?
Regards
-roja
On Mon, 7 May 2018, 14:33 ABEL Stephane, <Stephane.ABEL.cea.fr> wrote:
> Hi Roja,
>
> I do not know why you asked your question in the Amber Mailing list for a
> problem "not" related to Amber (in particularly if you want to use after
> GROMACS). That being said, to build a peptide with a defined number of AAs
> and particular conformation you could use
>
> ProBuilder : http://nova.disfarm.unimi.it/probuilder.htm
> PeptideBuilder a python script :
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3661355/
>
> and then use pdb2gmx, etc....
>
> 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 : dimanche 6 mai 2018 15:29
> À : AMBER Mailing List
> Objet : Re: [AMBER] Poly amino acid helix form topology files
>
> I can't understand this part of manual, but all in all thank you so much.
>
> On Sun, 6 May 2018, 17:50 Carlos Simmerling, <carlos.simmerling.gmail.com>
> wrote:
>
> > I don't have experience with gromacs setup. For Amber you should look in
> > the Leap section of the manual at the impose command. You should also
> > search the mailing list archive for leap impose.
> >
> > On Sun, May 6, 2018, 9:15 AM roja rahmani <roja.rhmn.gmail.com> wrote:
> >
> > > Would you please directly refer me to the exact page and manual. Which
> > page
> > > directly refer to this issue?
> > > Then, i want its topology files for gromacs and not simulate in amber.
> > >
> > > Best
> > > -roja
> > >
> > > On Sun, 6 May 2018, 17:31 Carlos Simmerling, <
> > carlos.simmerling.gmail.com>
> > > wrote:
> > >
> > > > You can use the impose command in leap to build a helical backbone.
> See
> > > the
> > > > manual for details.
> > > >
> > > > On Sun, May 6, 2018, 2:53 AM roja rahmani <roja.rhmn.gmail.com>
> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I want to have poly threonine(10 threonine) but in helix form and
> > then
> > > > add
> > > > > NME and ACE add terminals. I draw it in PYMOL but there are some
> > > problems
> > > > > in structure which is not identified by amber.
> > > > >
> > > > > Is there any way to have this molecule in helux form directly in
> > amber?
> > > > And
> > > > > extract its .prmtop aand .incprd file Would you please help me?
> > > > >
> > > > > Best regards
> > > > > -roja
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Received on Mon May 07 2018 - 04:30:02 PDT
