A question on minimization

From: santanu chatterjee (santanu_c10_at_yahoo.co.in)
Date: Fri Nov 04 2005 - 15:44:32 CST

  I was trying to minimize solvated ww domain ( 39
 residues ). I do not know very well about the
 minimization procedure and what to expect at the end.
 I ran 200 steps of minimization. It looks like the
     protein molecule is
 being pushed at one side. Moreover there is a hole in
 the middle. I am not sure whether this is something I
 should expect after the minimization is complete. Any
 ideas, thoughts, hints will be most welcome since I
 have no idea why it should look like this after
 minimization or is it just some mistake in setting up
 the parameters. I have put the pictures of the
solvated molecule before and after minimization on the
web (http://www.nd.edu/~schatter/minimization). The
second picture clearly depicts the strange behavior.

 Thanks in advance,

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