On Mon, Oct 18, 2010, Raman Parkesh wrote:
> 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.
Generally, on would take the top "N" structures from CYANA (where "N" is a
couple dozen), and use those as starting points for Amber refinement.
> 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.
You can just keep ig=-1 for all runs; that will give you a random number seed
based on the time of day, which will be different for each run.
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 19 2010 - 03:30:04 PDT
