[gmx-users] Hbonds between Adenine and Thymine

[Justin Lemkul]

Please keep the discussion on the gmx-users list.

On 11/29/12 6:12 AM, Hovakim Grabski wrote:
> Dear Justin,
>
> When I try to select 10DA residue from one strand and 17DT from the other
> strand,I type r10 and r17 and both select 64 atoms, after r26 it selects water
> molecules.

You can easily check (using a text editor) which atoms make_ndx is choosing.  In 
theory, your approach is correct and very straightforward.  Can you please provide?

1. Your exact make_ndx command
2. A few lines from residue 10DA of whatever coordinate file you're using
3. The index group produced from residue 10

Did you renumber the file at any point, for instance, with pdb2gmx?  That is, 
whatever started out as residue 10 may not still be numbered as such in the 
topology and any resulting coordinate files produced from the simulation. 
Without knowing exactly what you're using as make_ndx input, it's hard to track 
down what's going on.

-Justin

> And then I check for Hbonds with g_hbond  I get 3 Hbonds, but between A and T
> they form 2 Hbonds?
> It seems I'm doing something wrong.
> What can I do in this case?
> Thanks in advance,
> Best regards,
> Hovakim
>
> --------------------------------------------------------------------------------
> *От:* Justin Lemkul <jalemkul at vt.edu>
> *Кому:* Hovakim Grabski <hovakim_grabski at yahoo.com>; Discussion list for GROMACS
> users <gmx-users at gromacs.org>
> *Отправлено:* четверг, 29 ноября 2012 1:33
> *Тема:* Re: [gmx-users] Hbonds between Adenine and Thymine
>
>
>
> 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
>
> ========================================
>
>

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

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

========================================