# YASARA MACRO
# TOPIC:       5. Structure Determination
# TITLE:       Fold an ensemble of NMR structures
# REQUIRES:    YASARA Structure and NMR Structure Determination Module
# AUTHOR:      Elmar Krieger, Sander Nabuurs, Chris Spronk
# LICENSE:     GPL
# DESCRIPTION: This macro folds a structure from the stretched-out conformation using NMR restraints

# To fold a structure, you need:
# - The protein sequence, in FASTA or PDB format,
#   default filenames are 'sequence.pdb' or 'sequence.fasta'
# - A file with distance and dihedral angle restraints,
#   default filename is 'restraints.tbl'
#
# You can either set the target by clicking on Options > Macro > Set target,
# or by uncommenting the line below and specifying it directly.
#macrotarget = 'c:\MyProject\1crn'

# If you want to change the defaults, do it here, before the defaults are included.
# (look in nmr_setdefaults to see what you can change)

# Set those defaults that have not been set already
include nmr_setdefaults

# Step 1: Fold the stretched out conformation to arrive at an approximate fold
# ============================================================================
# Especially for larger proteins, the result is far from accurate, but well
# suited to arrive at the real structure during a molecular dynamics simulation.

Clear
# Write the log
LogAs (logfile),append=no,print 'Folding (structures) structures from the sequence `(seqfile)` using restraints `(restrainfile)`' 
# Build a linear peptide chain
BuildMol (seqfile)
Clean
Style Tube
# Set the BFactors for floating assignment
BFactorAtom (floating),25
# We need a forcefield with knowledge based potentials for sampling
ForceField YASARA
SimSteps 500
# Set restraining potential and parameters
RestrainPot (defaultpot)
RestrainPar (defaultpar)
if correctcispro=='Yes' or correctcispro=='yes'
  # Cis-prolines are not allowed. We therefore exclude the peptide bonds
  # before prolines from sampling by fixing the C and N atom:
  FixAtom N Res Pro
  FixAtom C with bond to N Res Pro
# Fold the structures from the stretched out conformation
Experiment NMRFolding
  # The object to fold
  StartObj 1
  # The file(s) with NMR restraints (default extension is .tbl)
  RestrainFile (restrainfile)
  # The number of structures to generate
  Structures (structures)
  # The filename for the structures (digits will be incremented)
  StructureFile (ensemblefile)(start)
# Generate the initial structures
Experiment On
Wait ExpEnd