On 11/28/12 3:43 PM, Hovakim Grabski wrote:
Dear Gromacs users,
I set a  simulation of 26 base pairs  of  DNA with Ethidium Bromide for 5 ns.
After a while Thymine rotated for about 70 degrees and then returned to its 
initial position.
I wanted to find out hbonds between Adenine and Thymine but with make_ndx 
things don't work so well.
How can I select Adenine from one strand and Thymine from the other strand and 
then run g_hbond ?

You can use make_ndx to select any residues you want. You'll have to describe exactly what you did that produced insufficient results. Saying it didn't work well doesn't tell us anything, because it is in fact quite easy to produce usable index groups.

-Justin

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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