# Sample config file for QRNA 0.2
# Just uncomment the lines you need.

#INPUTPDB   ./1DUP.pdb
#OUTPUTPDB  ./1DUP_refined.pdb
#WRITEFREQ  1000    # Frequency of writing outputpdb (each xxx steps); by default 100
#TRAJECTORY 1       # {0,1} - Each outputPDB is written to a separate file; by default OFF

VERBOSE 1

NSTEPS     5000   # Maximal number of steps; by default 100000
#CUTOFF     12.0    # Cutoff for van der Waals [Ang]; by default 12
#USEBORN    1       # {0,1} - Born electrostatix, i.e. implicit solvent (off/on); by default OFF
#ELECTR     0       # {0,1} Electrostatics (off/on); by default ON
#VDW        0       # {0,1} Van der Waals interactions (off/on); by default ON

#HBONDS     0       # {0,1} Hydrogen bonds (off/on); by default ON
                    # They are necessary to autodetect secondary structure.

#SSDETECT   0       # {0,1} - Detect base pairs automatically, by default ON
#SSCONSTR   0       # {0,1} - Impose constraints on base pairs (off/on); by default ON

#MAXSTEP    1e-8    # Max step size for golden section search; by default 1e-4
#MINSTEP    1e-10   # Min step size for golden section search; by default 1e-8
                    # (In most cases these are parameters not to fuck with)

NUMTHREADS  08      # Number of threads (parallel builds only!); by default 4
                    # Takes no effect in sequential builds of QRNA.
                    # Only calculations of electrostatics are currently parallelized.

#BLOWGUARD  0       # Protection against explosion due to high stress; by default ON
                    # It slows the minimization!

#POSRESTRAINTS 1    # {0,1} - Positional restraints (off/on), read from occupancy and beta-factors;
                    # by default OFF

# Secondary structure can be specified in two ways.
# The deprecated and retarded way is via Vienna notation. It applies to the first chain only:
#SECSTRUCT   (((....)))
# The kosher and robust way is via pairwise restraints specified in a separate file:
#RESTRFILE file_with_restraints.txt