Thanks David. I actually kept ig=-1 and it worked fine. I will now take top
20 structure with very low rmsd difference.
Raman
On 19 October 2010 05:59, David A. Case <case.biomaps.rutgers.edu> wrote:
> 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
>
>
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Received on Tue Oct 19 2010 - 06:30:03 PDT
