AMBER Archive (2003)

Subject: RE: AMBER: aminoacid mutation

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Oct 27 2003 - 23:09:23 CST

There might be a useful lead in these pages:

  http://ccl.osc.edu/cca/archived-messages/92/10/12
  http://www.compchemcons.com/publications/polsil.htm

Bill Ross

        LEU -> ALA mutation is simple. But ALA -> LEU can be a bit tricky if it
        has to potential to bump into other neighboring atoms.
        
        yong
        
        -----Original Message-----
        From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
        Of Ioana Cozmuta
        Sent: Monday, October 27, 2003 7:46 PM
        To: Amber List
        Subject: AMBER: aminoacid mutation
        
        
        Hi amber users,
        
        Is there a way to "automatically" mutate an aminoacid from a protein
        structure into another one. Say I want to replace an ALA aminoacid with
        a
        LEU aminoacid. Is it possible just to select the ALA aminoacid I want to
        mutate and turn it into LEU? Is there some software out there that
        could do this on a more automatic basis?
        The way I thought doing it was to edit the pdb file myself and try to
        edit
        the coordinates of the atoms in the new aminoacid such that the bond
        lengths are preserved and then equilibrate the new positions. But then
        my
        boss told me to try "not to lose time with this" and find a software
        that
        does it automatically :)
        
        Any suggestions are welcomed!
        Thanks,
        Ioana
        
        
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