[gmx-users] Generation of the Distance Restraints
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.
> 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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