You can use the bond command but the initial structure will probably be
extreme distorted. In my experience minimization to fix it can lead to many
other problems that are even harder to fix like isomerization.
On Oct 18, 2016 7:25 PM, "Thakur, Abhishek" <axt651.miami.edu> wrote:
> Thank you so much.
>
>
> I also want to know is there any way that I can join N terminal and C
> terminal of my peptide while make the structure from sequence.
>
>
> It means I have a sequence and I would like to make a cyclic peptide out
> of it.
>
>
>
> Thanking you,
>
> Abhishek
>
> ________________________________
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Tuesday, October 18, 2016 11:37:46 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] how to make peptide
>
> You can also try 'makestructure' or "permutedihedrals" command in cpptraj:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__archive.
> ambermd.org_201609_0345.html&d=DQICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
> 0Hah93XWYYBgmROOVcaccg&m=fHKvx8xUZqMAySXFB8Eno0GkrxoArMBWnP3scas8vvQ&s=
> cofbFGchMaGuZ3ovCNY4jRh3iDh-EXu2NHKz_lcz9uU&e=
>
> Hai
>
> On Tue, Oct 18, 2016 at 6:26 PM, Thakur, Abhishek <axt651.miami.edu>
> wrote:
>
> > Thank you so much.
> >
> >
> > ________________________________
> > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Sent: Tuesday, October 18, 2016 11:21:08 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] how to make peptide
> >
> > You can use the impose command in leap to force certain dihedral angles,
> or
> > you could do md with some restraints. A lot depends on the details of
> what
> > you are trying to do.
> >
> > On Oct 18, 2016 6:19 PM, "Thakur, Abhishek" <axt651.miami.edu> wrote:
> >
> > > Hi Carlos,
> > >
> > > Thank you so much,
> > >
> > > It works fine.
> > >
> > > Now I have another query,
> > >
> > > Now the peptide which has been created in linear, I want to make it "U"
> > > shaped.
> > >
> > > Can you suggest me the method by which I can do it?
> > >
> > > ________________________________
> > > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > > Sent: Tuesday, October 18, 2016 10:54:03 AM
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] how to make peptide
> > >
> > > Leap will do this, check the tutorials and the manual.
> > >
> > > On Oct 18, 2016 5:52 PM, "Thakur, Abhishek" <axt651.miami.edu> wrote:
> > >
> > > > Hi everyone,
> > > >
> > > >
> > > > I am sorry for posting this question here.
> > > >
> > > > I have a sequence of amino acid, can anyone suggest me a software to
> > > > design create that peptide?
> > > >
> > > >
> > > >
> > > > Thanking you,
> > > >
> > > > Abhishek
> > > >
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Received on Tue Oct 18 2016 - 17:00:02 PDT
