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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