# YASARA MACRO
# TOPIC:       5. Structure Determination
# TITLE:       Set default parameters for NMR structure determination
# REQUIRES:    YASARA Structure and NMR Structure Determination Module
# AUTHOR:      Elmar Krieger, Sander Nabuurs, Chris Spronk
# LICENSE:     GPL
# DESCRIPTION: This macro is included by others to set default parameters

# If you make changes here, they will globally affect all NMR macros.
# The 'count' function checks if a variable has been defined before, and is used
# to make sure that none of the local settings you made are overwritten here.

if not count seqfile
  # The sequence filename (can have either .fasta or .pdb extension)
  # If a PDB file is given, it must contain a SEQRES record
  seqfile='(MacroTarget).fasta'

if not count firstresnum
  # Number of first residue in seqfile above. Increase if you don't want to model floppy
  # N-terminal residues, but still keep the official residue numbering for restraints.
  firstresnum=1
  
if not count restrainfile
  # The restraint filename. If you have multiple files, simply concatenate them first
  restrainfile='(MacroTarget).nef'
  restrainformat='nef'
  found = FileSize (restrainfile)
  if not found
    restrainfile='(MacroTarget).tbl'
    restrainformat='tbl'

if not count restrainformat
  RaiseError "If you set a restraint filename 'restrainfile', you also need to specify its format 'restrainformat', either 'tbl' (XPLOR) or 'nef'."

if not count nameformat
  # The atom name format in the restraint file: XPLOR, PDB, PDB3, PDBRev, YASARA or IUPAC
  if restrainformat=='tbl'
    nameformat='XPLOR'
  else
    nameformat='IUPAC'

if not count ensemblefile
  # The ensemble filename
  ensemblefile='(MacroTarget)'

if not count structures
  # The number of structures to generate in the ensemble
  structures=10

if not count foldmul
  # The initial folding from the stretched-out conformation is done 'structures*foldmul' times,
  # of which only the best 'structures' are kept for refinement. This makes sure that very bad
  # and hard to correct structures with knots etc. can be discarded before refinement.
  # Increase 'foldmul' if you find proteins with incorrect topologies in the final ensemble.
  foldmul=2

if not count ph
  # The pH at which the NMR spectrum was recorded.
  # (This information will be used in the final explicit solvent refinement step via
  # 'Experiment Neutralization' to assign protonation states of Asp, Glu and His residues).
  ph=7.4

if not count defaultpot
  # The normal restraining function (see RestrainPot command)
  defaultpot='SoftSquare, SqConstant=1.00, SqOffset=0.00, SqExponent=2, rSwitch=1.00, '+
             'SoExponent=1, Asymptote=2.00, RDCForceConst=1.00, RDCErrorScale=1.00'

if not count defaultpar 
  # The normal restraining parameters (see RestrainPar command)
  defaultpar='Average=Sum, Ceil=9999, DisMin=-1, Monomers=1, JoinDis=-1, FloatGroups=10%'
  
if not count defaultscale 
  # The normal scaling factors for distance, dihedral and RDC restraints
  defaultscale=25,2,1

if not count strongscale 
  # The strong scaling factors for distance, dihedral and RDC restraints
  strongscale=50,5,2
    
if not count violdismax
  # The maximum allowed distance restraint violation in A, 9999 to ignore
  violdismax=0.5
  
if not count violdihmax
  # The maximum allowed dihedral angle restraint violation in degrees, 9999 to ignore
  violdihmax=5

if not count violrdcmax
  # The maximum allowed dipolar coupling violation in Hz, 9999 to ignore
  violrdcmax=10

if not count correctoldcisiso
  # Flag if old cis-peptide bonds and wrong isomeres that are present from the beginning
  # should be corrected too. The default 'No' corrects only those newly formed during
  # high-temperature annealing and thus permits to solve structures with unusual
  # features like D-amino acids, provided that they are present in the input structure.
  correctoldcisiso='No'

if not count correctcispro
  # Flag if cis-peptide bonds before prolines should be corrected.
  # If you do not want to potentially miss a cis-proline in your structure,
  # set this flag to 'No'. If the lowest energy structures in the ensemble
  # then all have a certain cis-proline, fix it in the cis-conformation.
  # In any case, create a new ensemble with the flag set to 'Yes' to avoid
  # a random collection of cis-prolines.
  correctcispro='Yes'

if not count cysbridgelist
  # Treatment of cysteine bridges:
  # Option 1: Assign them automatically, bridge cysteines close in space
  cysbridgelist()='Auto'
  # Option 2: Explicity link the specified pairs of cysteine residues (example 1CRN)
  #cysbridgelist()=3,40, 4,32, 16,26
  # Option 3: Don't form cysteine bridges
  #cysbridgelist()='None'
  
if not count floating
  # Floating assignment
  # Option 1: No floating assignments
  floating='None'  
  # Option 2: All hydrogens 
  # floating='Element H'

if not count fofvacuo
  # The force field used for simulations in vacuo
  fofvacuo='NOVA'
  
if not count fofsolvent
  # The force field used for simulations in explicit solvent
  fofsolvent='YASARA'

if not count solventsimsteps
  # The number of simulation steps during refinement in explicit solvent
  # This mainly needs to be increased if you skipped preceding steps
  solventsimsteps=30

if not count solvent
  # The solvent to use for explicit solvent refinement. Either 'HOH' or 'DMSO'
  solvent='HOH'

if not count fofscale
  # Scaling factor for the force field energy when sorting the final ensemble
  # (due to electrostatics and solvation, force field energies are on a larger
  #  scale than restraint violation energies. If they were not scaled down, even
  #  structures with large restraint violations could be ranked first if they
  #  had excellent electrostatics).
  fofscale=0.1
  
if not count logfile
  # The log filename
  logfile='(MacroTarget).log'

if not count start
  # The number of the structure to start with:
  # If you remove the leading zeroes, you must make sure that the MacroTarget
  # does not have a terminal number. Also note that leading zeroes ensure that
  # file lists are correctly sorted when browsed in Explorer, Finder etc.
  start=001
   
# Slow down atoms moving faster than 10000 m/s to avoid simulation failures
# caused by bumps and incompatible restraints. This allows for larger time-steps.
Brake 10000