[gmx-users] Generation of the Distance Restraints

James Starlight jmsstarlight at gmail.com
Fri Mar 16 08:39:50 CET 2012

> 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 ?

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