VMD-L Mailing List

From: Kartheek (kartheek.p_at_research.iiit.ac.in)
Date: Mon Jul 18 2011 - 07:09:02 CDT

Hi all,
I am studying Hydration Dynamics of nucleic acids, Trying to plot radial distribution function of oxygen atoms of phosphate back bone w.r.t oxygen atoms of water by using VMD plugins,but unable to succeed
Steps which i have followed are
1.Loaded PSf file
2.Loaded DCD file
3.Analysis ---> Radial distribution function(RDF)

under RDF there are two options shown
Selection 1:
selection 2:

In selection 1, I have specified as "oxygen atoms of phosphate backbone"
In selection 2,I have specified oxygen atoms of water
 when i am executing this, it is showing some error in selection phrase,please tell me what is the correct phrase i have to use.
Any help from you will be highly appreciated.
thanks in advance.

From,
Pitta kartheek.