Big-QM

How to set-up big-QM calculations (all via. the changepdb program)

The big QM calculations construct a system that includes:

1) All residues within 4.5 Å to 6 Å

2) All buried charges

3) All junctions are moved 3 residues away from the "usual" small QM system
 * 1) Start from an pdb (p file that contains an optimised system (with comqum). Copy this file along with the syst1 file that was used to set-up the system. Rename syst1 to s1.
 * 2) Run changepdb on command "bc" on pdb3.pdb