Thank you so much Carlos.
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Wednesday, October 19, 2016 2:23:42 AM
To: AMBER Mailing List
Subject: Re: [AMBER] how to make peptide
Amber may not be the right tool for peptide design. If you want to know the
conformations of a specific peptide in solution, you might be able to do
that in Amber. Designing a sequence to bind well to a protein interface is
very different though. You might look into protein peptide docking tools,
or protein design tools.
On Oct 19, 2016 9:12 AM, "Thakur, Abhishek" <axt651.miami.edu> wrote:
> For now we are trying to design some cyclic peptide which can inhibit
> protein dimerization and study its interaction
> Sent using OWA for iPhone
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Tuesday, October 18, 2016 2:05:40 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] how to make peptide
>
> What do you want to learn from the simulations? That will help with
> design.
>
> On Oct 18, 2016 7:56 PM, "Thakur, Abhishek" <axt651.miami.edu> wrote:
>
> > Then what should I do?
> >
> > Any suggestion?
> >
> > ________________________________
> > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Sent: Tuesday, October 18, 2016 12:43:47 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] how to make peptide
> >
> > 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=fHKvx8xUZqMAySXFB8Eno0GkrxoArM
> BWnP3scas8vvQ&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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> > > uYmhgFWijp_IQN0DhA&r=
> > > > > 0Hah93XWYYBgmROOVcaccg&m=gwlojOiqEkRJnS9jiCn25Clxjy9dem
> > > > XTFXuw2hmO27E&s=tI-
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> > > > > >
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> > > > XTFXuw2hmO27E&s=tI-
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> > > > 0Hah93XWYYBgmROOVcaccg&m=HJlY5DigYsR9tvm631eo6pSQs4iuoc
> > OI3yFuJBDxxDU&s=
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> > OI3yFuJBDxxDU&s=
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> uYmhgFWijp_IQN0DhA&r=
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> > > BWnP3scas8vvQ&s=PYfCW5H382Mn_1B2tL0dpriIPxuQLecsGEy9behVQ4Q&e=
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> uYmhgFWijp_IQN0DhA&r=
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Received on Wed Oct 19 2016 - 07:00:02 PDT
