# YASARA MACRO
# TOPIC:       4. Molecular modeling
# TITLE:       Running an energy minimization
# REQUIRES:    Dynamics
# AUTHOR:      Elmar Krieger
# LICENSE:     GPL
# DESCRIPTION: This macro runs an energy minimization of the soup. Compared to the normal minimization experiment, it temporarily adds a water shell so that all force fields can be used directly, also those optimized for use with explicit solvent

# Clean the soup
Clean
# Make sure we have a cell
cellfound = CountObj SimCell
if !cellfound
  Cell Auto,Extension=12
# Make sure that at least one atom is free to move
fixedatoms = CountAtom fixed
if fixedatoms==Atoms
  RaiseError "All atoms are currently fixed, which makes an energy minimization impossible. Click Simulation > Free > All first."
# Specify the minimization convergence in kJ/mol
EnergyUnit kJ/mol

fof = ForceField
if fof!='NOVA'
  # Force field for explicit solvent
  # Do we already have enough waters present?
  waters = CountRes Water
  srfacc = SurfRes !Water,accessible
  if not waters or srfacc/waters>15
    # No, create and minimize water shell
    Experiment Neutralization
      NaCl 0
      Speed fast
    Experiment On
    Wait ExpEnd
    DelRes Water with distance>6 from !Water
  else
    # Remember which atoms have been fixed
    fixedlist() = ListAtom fixed
    # Fix everything except water
    Fix
    FreeRes Water
    # Energy minimize first the water alone
    ShowMessage "Running quick energy minimization of water molecules..." 
    Experiment Minimization
      Convergence 0.1
    Experiment On
    Wait ExpEnd
    # Fix those atoms that were fixed by the user before
    Free
    if count fixedlist
      FixAtom (join fixedlist)
# Main energy minimization
ShowMessage "Running main energy minimization..."
Experiment Minimization
  # Converge as soon as the energy improves by less than 0.05 kJ/mol per atom during 200 steps
  Convergence 0.05
Experiment On
Wait ExpEnd
# Final check that minimization did not introduce errors
wronghands = Check Isomers
cisbonds = Check PepBonds
if wronghands or cisbonds
  ShowMessage 'WARNING - There are (0+wronghands) wrong isomers and (0+cisbonds) cis-peptide bonds. Try again with automatic correction...'
  Wait ContinueButton
HideMessage