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 - 03:30:02 PDT
