[gmx-users] Hbonds between Adenine and Thymine

[Erik Marklund]

Hi,

A general note: make_ndx and index files are not magical in any way. You can usually construct an index group from e.g. a pdb file with awk. It's just lists of atom indices.

Best,

Erik

28 nov 2012 kl. 22.33 skrev Justin Lemkul:

> 
> 
> 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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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
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