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 - 16:30:03 PDT
