If you want to model DNA without worrying about restraints with protein or something else, Modeller is not the best tool to use. Take your pick from the links below:
http://rutchem.rutgers.edu/~xiangjun/3DNA/ http://www.t10.lanl.gov/namot/ http://www.scripps.edu/mb/case/casegr-sh-3.2.html http://www.homepage.montana.edu/~mdlakic/software.html
If molecules built end up being slightly irregular, there is a script to fix that assuming one has CNS:
http://www.dl.ac.uk/list-archive-public/ccp4bb/2005-01/msg00420.html
Hope this helps,
Mensur
At 07:28 PM 6/22/2005, you wrote: >Maybe Modeller won't even be necessary for this task, >but, anyway, someone can point a simpler solution: how >can I generate a PDB for a small DNA double helix >(something like 10-15 base pairs)? > >Lucas
========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic@montana.edu | ==========================================================================