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 - 03:30:02 PDT
