On Fri, Apr 26, 2013, Sangita Kachhap wrote:
> For use of distance restraint there is requirement of a file that
> contatin restrint which to be applied and for generation of this
> restraint file there is requiremt of 7 column file that contain:
> 1st_res# 1st_res_name 1st_atom_name
> 2nd_res# 2nd_res_name 2nd_atom_name upper_bound
>
> Value in last column i.e. uper_bond, from where this value taken and what is
> this value?
First: this is not a "requirement": the makeDIST_RST program can be helpful if
you already have information in the format listed above (generally from NMR
analysis programs). You can alway write sander restraints "by hand", and that
is the most flexible approach, and often the best if you only have a few
restraints.
Second, "upper_bound" is the upper bound on the distance between the two
atoms. It often comes from NMR, but can also be the result of modeling, or
can be based on other information or hypotheses.
...dac
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Received on Fri Apr 26 2013 - 17:30:03 PDT
