Example: QMMM with capping atoms
********************************

This is an example of QMMM using capping atoms. Capping atoms are
added automatically when bonds are broken (between the QM and MM
region). Because the amber forcefield is used the
"AtomicInfoForCappingAtom" needs to be set, as the default type "H" is
not an AMBER type.

"Download QMMM_Butane.run"

   #! /bin/sh

   "$AMSBIN/ams" <<eor

   Task GeometryOptimization

   GeometryOptimization
       Convergence Gradients=1E-4
   End

   System
       Atoms
           C  0.0000  0.0000  0.0000  region=QM  ForceField.Charge=0.0  ForceField.Type=CT
           H  1.0910  0.0000  0.0000  region=QM  ForceField.Charge=0.0  ForceField.Type=HC 
           H -0.3598  1.0300  0.0000  region=QM  ForceField.Charge=0.0  ForceField.Type=HC 
           C -0.5021 -0.7074 -1.2586  region=QM  ForceField.Charge=0.0  ForceField.Type=CT
           H -0.1397 -1.7383 -1.2662  region=QM  ForceField.Charge=0.0  ForceField.Type=HC 
           H -1.5949 -0.7053 -1.2662  region=QM  ForceField.Charge=0.0  ForceField.Type=HC 
           H -0.1307 -0.1841 -2.1433  region=QM  ForceField.Charge=0.0  ForceField.Type=HC 
           C -0.5195 -0.7318  1.2374  region=MM  ForceField.Charge=0.0  ForceField.Type=CT
           C -0.0376 -0.0530  2.5227  region=MM  ForceField.Charge=0.0  ForceField.Type=CT
           H  1.0524 -0.0554  2.5580  region=MM  ForceField.Charge=0.0  ForceField.Type=HC 
           H -0.3994  0.9752  2.5580  region=MM  ForceField.Charge=0.0  ForceField.Type=HC 
           H -0.4230 -0.5961  3.3860  region=MM  ForceField.Charge=0.0  ForceField.Type=HC 
           H -0.1631 -1.7630  1.2286  region=MM  ForceField.Charge=0.0  ForceField.Type=HC 
           H -1.6105 -0.7355  1.2286  region=MM  ForceField.Charge=0.0  ForceField.Type=HC 
       End
       BondOrders
           1 2  1.0
           1 3  1.0
           1 8  1.0
           1 4  1.0
           8 14 1.0
           8 13 1.0
           8 9  1.0
           4 5  1.0
           4 6  1.0
           4 7  1.0
           9 12 1.0
           9 11 1.0
           9 10 1.0
       End
   End

   Engine Hybrid
       QMMM
           QMRegion QM
           QMEngineID ADF
           MMEngineID ForceField
       End

       Capping
           AtomicInfoForCappingAtom ForceField.Type=HC ForceField.Charge=0.0
       End

       Engine ADF
         Basis
           Type DZP
         End
         Relativity
           Level None
         End
       EndEngine
       
       Engine ForceField
         Type Amber95
       EndEngine
   EndEngine

   eor
