Thank you Daniel and Hai
On Tue, Aug 8, 2017 at 12:53 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> On Mon, Aug 7, 2017 at 10:28 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > You could try using the 'makestructure' command in cpptraj (or pytraj
> > if you like python).
>
>
> .Rajarshi
> some examples in pytraj:
> http://amber-md.github.io/pytraj/release/2.0.0/_api/
> pytraj.html?highlight=make_structure#pytraj.make_structure
> (see Examples section)
>
> Hai
>
>
>
> > It can be used to rotate protein backbone
> > dihedrals into pre-set conformations or it can be used with a
> > reference structure as a template. Note that this command won't do
> > anything fancy like optimize side chain positions, but feel free to
> > experiment. See the manual for more details.
> >
> > -Dan
> >
> > On Thu, Aug 3, 2017 at 12:34 AM, Rajarshi Roy <phd1701171011.iiti.ac.in>
> > wrote:
> > > Can you please tell how to align the peptide chain side by side so
> that
> > > they can form hydrogen bond.
> > >
> > > On 02-Aug-2017 10:56 PM, "Hai Nguyen" <nhai.qn.gmail.com> wrote:
> > >
> > > I think you need them connect via natural hbond or you need to create
> > > restraints in your simulation.
> > >
> > > On Wed, Aug 2, 2017 at 12:32 PM Rajarshi Roy <phd1701171011.iiti.ac.in
> >
> > > wrote:
> > >
> > >> Hi
> > >> No. I want to create hydrogen bond between two peptide chain. And
> > also i
> > >> want to create array peptide chain like beta strand
> > >>
> > >> On 02-Aug-2017 9:59 PM, "Hai Nguyen" <nhai.qn.gmail.com> wrote:
> > >>
> > >> > Yes. tleap can add hydrogen and missing atoms
> > >> >
> > >> > Hai
> > >> >
> > >> > On Wed, Aug 2, 2017 at 10:51 AM Rajarshi Roy <
> > phd1701171011.iiti.ac.in>
> > >> > wrote:
> > >> >
> > >> > > Hi,
> > >> > > I created a modified short peptide and want to create beta
> > > strand
> > >> > > like structure of 3-8 residue.I build that modified peptide
> using
> > >> > > avogadro. How can I create hydrogen bond between that peptide to
> 3
> > to
> > >> 8
> > >> > > array of that?
> > >> > > Can it be done using amber or other.?
> > >> > > _______________________________________________
> > >> > > 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Laboratory of Computational Biology
> > National Institutes of Health, NHLBI
> > 5635 Fishers Ln, Rm T900
> > Rockville MD, 20852
> > https://www.lobos.nih.gov/lcb
> >
> > _______________________________________________
> > 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
>
--
with regards
Rajarshi Roy
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 08 2017 - 04:00:02 PDT
