AMBER Archive (2004)

Subject: AMBER: Amber & mutation

From: bybaker_at_itsa.ucsf.edu
Date: Wed Jun 09 2004 - 19:53:58 CDT


Hello, Amber:

I mutated a structure model using SwissPDB Viewer. Two residues at helix
regions were selected as targets. The two residues are located in the
middle of the helix, and just 6 amino acids away. These two residues were
replaced by PRO (prolines). The mutated model is named as ‘pro2’. Pro2
was then subjected to energy minimization in sander. The input file is:

‘ Energy minimization run 1b
   &cntrl
      imin=1, ncyc=250, maxcyc=500, ntb=0,
    &end’

The resulted .rst file was used to generate .pdb file, named as
‘pro2min1’. When I looked at ‘pro2min1’, no structure change was made in
the helix region. Do prolines suppose to break the a-helix structure? If
they do, energy minimization supposes to fix the bad contacts, and result
to changed helix structure? Or the current structure modeling methods
can’t perform real conformational change of a protein.

Any advices will be very appreciated.

Regards

Bo Yang

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