[gmx-users] Generation of the Distance Restraints

Mark Abraham Mark.Abraham at anu.edu.au
Fri Mar 16 08:56:30 CET 2012

On 16/03/2012 6:39 PM, James Starlight wrote:
>>     2) Also I've found that there is more simple way to define
>>     restraines based on the BONDS enty in the topology file. Could
>>     you provide me with the more information about this simpler way ?
>     Simpler, but not a restraint to within a region. The manual
>     section we are discussing links you to the available documentation
>     elsewhere in the manual. I don't have the time to help with every
>     interpretation question you might have.
>     Mark
> Mark,
> In more details I want to generate network of disres for all helices 
> H-bonds. So I want to restraint H-bond distance between i and i+4 
> atoms of the backbone.
> What is the simplest way to do such task? I think that the ussage of 
> genrestr -disre could be useful for such generation of the complex 
> disres because of the size of my protein. But how I could define the 
> restrained atoms (i, i+4 atoms ) ? In the make_ndx options I didnt 
> find the most trivial sollution of the such choise. So the only 
> sollution is to define each I and I+4 atoms of the backbone manualy, 
> isnt it ?

Solving that will require some scripting. Because you know from genrestr 
-h that a half a matrix of distance restraints are generated for the 
index group chosen, and you only want i->i+4 restraints, you'll need a 
separate index group for every i->i+4 pair. So you can write a script 
that loops over calls to make_ndx to create a group of 2 atoms that are 
a suitable atom from i and i+4. Making make_ndx non-interactive (to call 
it from a script) is described on the website. Making a shell script to 
do that is a skill you will need to learn elsewhere.

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