Hi,
You could try using the 'makestructure' command in cpptraj (or pytraj
if you like python). 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
Received on Mon Aug 07 2017 - 07:30:03 PDT
