Re: [AMBER] cyclic peptides

From: David A Case <>
Date: Sun, 30 Aug 2015 21:13:33 -0400

On Sun, Aug 30, 2015, Lara rajam wrote:

> I am able to generate the top and inpcrd files for a solved cyclic
> peptides structures .


> Is it possible to build a cyclic peptide by giving the sequence in leap !

No: LEaP is not really a model-building program. If you just give
a sequence of a linear peptide to LEaP, it can build an extended
conformation, which is sometimes useful (although not for cyclic
systems!). But generally, if you don't have a starting structure, you
need to create one, generally with some non-Amber program.

The distance geometry facility in NAB is one way to build non-trivial
structures. But you may want to use some more specialized program, suited to
cyclic peptides. If you have access to a solved structure of a peptide
similar to the one you are interested in, that might be a good starting point.


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Received on Sun Aug 30 2015 - 18:30:03 PDT
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