Re: [AMBER] NAB : Orienting a molecule

From: Aldo Segura <>
Date: Fri, 4 Oct 2013 12:53:09 -0700 (PDT)

Dear Himanshu,

I'm not sure to follow you, but you should take a look on the Tutorial B1 at Amber Tutorials website (



Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7013, Cincinnati OH 45229

Para: AMBER Mailing List <>
Enviado: Viernes, 4 de octubre, 2013 14:33:48
Asunto: [AMBER] NAB : Orienting a molecule

Dear friends,

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 tried in xLeap but found it difficult to do, then I looked for a NAB
module. Here also I couldn't find a way to align the entire molecule
to a line. I went through NAB direction in Ambertools manual (Program 3 )
but couldn't resolve it.

Kindly help me to get away from it

Thanks in advance.

*With Regards,
Graduate Scholar, Center for Condense Matter Theory
Department of Physics IISc.,Bangalore India 560012*
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Received on Fri Oct 04 2013 - 13:00:07 PDT
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