> I mutated one residue in my protein from LYS to SER using PyMol.
> Following the mutations, I performed a minimization step with the two
> upstream and downstream residues from the mutated one unrestrained.
> However even after 30000 minimization steps, the structure did not seam
> to have changed a lot. Is there any particular way to sample the entire
> configuration space when doing mutations? Or is there any method to
> perform these mutations in amber rather than PyMol?
Minimization does virtually nothing to explore configuration space.
Dynamics is the way to do this in Amber.
Bill
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Received on Fri May 21 2010 - 09:30:03 PDT
