[gmx-users] Hbonds between Adenine and Thymine

Justin Lemkul jalemkul at vt.edu
Wed Nov 28 22:33:42 CET 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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