AMBER Archive (2003)

Subject: Re: helix axis for A-RNA

From: M. L. Dodson (bdodson_at_scms.utmb.EDU)
Date: Tue Jun 10 2003 - 08:36:44 CDT

Vlad Cojocaru writes:
> Dear coleagues,
> I have an RNA molecule that comprises two helical regions and one
> loop and I would like to follow the agle between the 2 helices during an
> MD trajectory. I was thinking to represent the helical axis of the two
> helices and then calculate the angle between the 2 axis. I was trying
> with VMD to represent the helical axis but yet I didnt have a lot of
> success. If somebody knows how coould one define and represent the
> helical axis of an A type RNA helix within VMD or other software I would
> kindly appreciate any suggestions.
> Best wishes,
> vlad
>
> --
> Vlad Cojocaru
> Max Planck Institute for Biophysical Chemistry
> Department: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1327
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
> home tel: ++49-551-9963204

I have had good luck using nab from the Case laboratory for
these kinds of one-off computations (and for many other molecular
modeling activities, as well). http://www.scripps.edu/case/

Bud Dodson 

-- 
M. L. Dodson                                bdodson_at_scms.utmb.edu
409-772-2178                                FAX: 409-772-1790