Re: [AMBER] how to make peptide

From: Thakur, Abhishek <axt651.miami.edu>
Date: Tue, 18 Oct 2016 22:26:39 +0000

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=gwlojOiqEkRJnS9jiCn25Clxjy9demXTFXuw2hmO27E&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=gwlojOiqEkRJnS9jiCn25Clxjy9demXTFXuw2hmO27E&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=
>
_______________________________________________
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=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 18 2016 - 15:30:03 PDT
Custom Search