Re: [AMBER] NAB : Orienting a molecule

From: Daniel Roe <>
Date: Fri, 4 Oct 2013 14:38:00 -0600


> I am trying to build a model with Nucleic acid where I would
> like to align the molecule (say 12 mer dna) to a particular line .

I'm not exactly sure what you mean by 'line', but you can align a
molecule along its principal axis in cpptraj or ptraj using the
'principal' action:

trajin mol.rst7
principal <mask> dorotation
trajout mol.rotated.rst7

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Oct 04 2013 - 14:00:09 PDT
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