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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 06 2018 - 06:30:03 PDT
