> 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 ? James
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