AMBER Archive (2002)

Subject: Re: building ss DNA/RNA

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 30 2002 - 17:29:19 CDT

On Tue, Jul 30, 2002, Cozmuta wrote:
>
> I am a new user of amber. I want to build using nukit single stranded
> homopolymers of DNA or RNA but I can not find the option that decides
> between building a double stranded or ss structure. I would appreciate
> your help.
>

You could just build a double strand, and throw away the second strand (by
editing the output pdb file). Nucgen doesn't have any special model for
single-stranded nucleic acids, and simulations suggest that just one side
of a ds model is reasonable as a *starting* structure.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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