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.
Mark
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