I have never done that. You can try googling 'make cyclic peptide amber'
Hai
> On Oct 18, 2016, at 7:24 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
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
>>> ambermd.org_mailman_listinfo_amber&d=DQICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
>>> 0Hah93XWYYBgmROOVcaccg&m=gwlojOiqEkRJnS9jiCn25Clxjy9dem
>> XTFXuw2hmO27E&s=tI-
>>> zJQkO1Zz3mMMPRTn93uoSY4vrjkQtI8IZfLyq2Q8&e=
>>>>
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>>> AMBER mailing list
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>>> ambermd.org_mailman_listinfo_amber&d=DQICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
>>> 0Hah93XWYYBgmROOVcaccg&m=gwlojOiqEkRJnS9jiCn25Clxjy9dem
>> XTFXuw2hmO27E&s=tI-
>>> zJQkO1Zz3mMMPRTn93uoSY4vrjkQtI8IZfLyq2Q8&e=
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
>> ambermd.org_mailman_listinfo_amber&d=DQICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
>> 0Hah93XWYYBgmROOVcaccg&m=HJlY5DigYsR9tvm631eo6pSQs4iuocOI3yFuJBDxxDU&s=
>> ITtls89XnJcIKtyNbEP_HU7HOZopB-rB6ajUFbk3ewk&e=
>>>
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>> AMBER mailing list
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>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
>> ambermd.org_mailman_listinfo_amber&d=DQICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
>> 0Hah93XWYYBgmROOVcaccg&m=HJlY5DigYsR9tvm631eo6pSQs4iuocOI3yFuJBDxxDU&s=
>> ITtls89XnJcIKtyNbEP_HU7HOZopB-rB6ajUFbk3ewk&e=
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>> AMBER mailing list
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>>
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Received on Tue Oct 18 2016 - 16:30:04 PDT
