3.4. Tricks of using "run.prm"
3.4.1. Detecting ligand
As the ligand bond distance is around 1.8 to 2.4 angstroms, we can take advantage of the clash report in step 1 of the mcce program. If $(CLASH_DISTANCE) is set to be 2.4, then run only step 1. The atom pairs within this distance will be reported.
3.4.2. Updating head3.lst
If you want to use different parameters such as reference pKa and reference reaction field energy in step 4 Monte Carlo sampling, you may edit step 3 output file "head3.lst". Another way to load new parameters and update "head3.lst" is to run step 3 without doing "Delphi". In another situation, if conformers are split into multiple directories to run the step 3, you need to "merge" them and update "head3.lst". To do this, make $(DELPHI_END) a smaller number than $(DELPHI_START) and run step 3 only. The self energy will be reloaded and updated based on the current parameters.
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