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.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.scms.utmb.edu
409-772-2178 FAX: 409-772-1790
Received on Tue Jun 10 2003 - 15:53:01 PDT
