| 11:06:42 AM PDT - Tue, Oct 22nd 2013 |
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| Thank you for your help! What is the best way to extract the PDB file and which file should I extract it from? I know for output from the Molecular Dynamics module, PDB files can be extracted from the trajectory file (*.trj) using the Analysis module. However, no trajectory file is created from the qmmm dft geometry optimization calculation, and it's unclear to me in which output file the final optimized coordinates can be found. If necessary, I can create a PDB formatted file from raw xyz coordinates, if I just knew how to access the coordinates.
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