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 <jalem...@vt.edu>
*Кому:* Hovakim Grabski <hovakim_grab...@yahoo.com>; Discussion list for GROMACS
users <gmx-users@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
========================================
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