HI
I would like to generate a series of nmr structure (generated from CYANA)
using distance restraint in AMBER. I was wondering what is the best protocol
for that
1) Do you take the all the structure (say from CYANA) and run RMD on each of
them.
2) or your take the lowest energy strucutre from CYANA, energy minimize it
and then generate a series of structure in AMBER using random seed
generation (e.g ig=-1). What is the best strategy for ig? should you set it
to -1 and then manually run the simulated annealing many times or should you
increase the ig value between each runs.
Thanks
Raman
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Received on Mon Oct 18 2010 - 15:30:04 PDT
