We will now make a very simple setup with a small piece of peptide, just to get something running.
Start ADFinput Go to the Protein panel Select the examples/PDB/pentapeptide.pdb file (after clicking on the Select button) Select one residue and put in in the QM region Save your set up (be sure not to include a solvent) Run your calculation
ADFtail will start, showing the logfile. The calculation starts, and after a few moments seems to be stuck in 'FRAGM'. At this point ADF is actually performing the MM optimizations, but this is not visible in the logfile. So, at this point, open the output file in ADFtail:
In ADFtail (the logfile window), use the File → Open command Select the output file (ending with .out)
Now you should see the MM optimizations. After 5000 iterations, they will stop, and the QM calculation will continue. Note that the QM geometry will not be optimized as we have not requested a Geometry Optimization.
