How can I get the final optimized coordinate PDB file after molecular mechanics optimization?

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3:10:49 PM PDT - Wed, Sep 12th 2012
The optimizatio should have provided a file "1IVD_opt.qrs" with the optimized geometry. Running prepare with: read 1IVD_opt.qrs write 1IVD_opt_final_1.pdb should give you what you need.