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
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Tue Jul 30 2002 - 15:29:19 PDT
