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.?
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> --
> -------------------------
> 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
>
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Received on Mon Aug 07 2017 - 12:30:02 PDT
