2010/2/25 Shaandar Nyamtulga <nyam100.hotmail.com>:
>
> I changed the sequence like this {NALA ALA ALA ALA CALA}. And added minimization cycle 10 times (2000). No success. And when I see original structure from xleap it is very strained structure, otherwise backbone is a line. At least Amber should be able to convert this linear backbone into a helix after EM. Thank you
2000 is still a small number of steps, but the point remains that the
sander minimizer will converge only to the closest local minimum.
While the linear conformation is certainly not the most stable
structure for a poly-alanine, it is not *strained* per se, since the
bonds/angles are in their equilibrium positions.
If you want to see your alanine 5-mer fold into a helix, you'll have
to run some form molecular dynamics (i.e. simulated annealing can be
shown to give the global minimum structure if done *correctly*).
You will not see what you're trying to see just doing a minimization, though.
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Feb 24 2010 - 23:00:02 PST
