# In this example, we create a hairpin with a three base pair stem and a four base loop.
# You can compare this to the tetraloop found in the large subunit of the yeast mitochondrial ribosome, PDB ID 5MRC, residues 2639 to 2648.

#sequence
RNA A 2639     UACGUAAGUA
readAtStage 1
# Turn on MD forces (incl. electrostatic and Lennard Jones forces)
setDefaultMDParameters
readBlockEnd



############
# Duplex Watson-Crick base pairing section
############
# You can impose WatsonCrick/WatsonCrick/Cis base pairing forces pulling residues 2656-2658 towards 2663-2665:
nucleicAcidDuplex A 2639 2641 A 2648 2646
# Note that in the above the first residue stretch is rising, the second is falling. This is because the strands are antiparallel. Respect this syntax!

# Or, equivalently, you can apply the base pairs individually::
#baseInteraction A 2641 WatsonCrick A 2646 WatsonCrick Cis 
#baseInteraction A 2640 WatsonCrick  A 2647 WatsonCrick Cis 
#baseInteraction A 2639 WatsonCrick  A 2648 WatsonCrick Cis

#In prior editions of MMB we set the helical stacking using baseInteractions which could be automatically applied. Let's turn those off now:
setHelicalStacking False
#Why? Because now we have a better way to make nice helices. And actually many other dinucleotide steps. Thanks to Emmanuel Peter, Bohdan Schneider, and Jiri Cerny, who implemented NtCs in MMB.

############
# NtC section
############
#The following imposes the NtC of type AA00 -- the most typical A-form stacking dinucleotide step -- to the dinucleotide formed by residues 2639 and 2640. The last parameter is a force constant:
NtC A 2639 2640 AA00 .5
# There are three stacked bases on this strand. So we impose a second NtC force, overlapping the prior one:
NtC A 2640 2641 AA00 .5
# And now we do the same thing on the other strand:
NtC A 2646 2647 AA00 .5
NtC A 2647 2648 AA00 .5

#Alternatively, you may use this more terse notation, basically you provide only the start and end residues and it applies a single NtC Class to the entire stretch:
#NtC A 2639 2641 AA00 .5
#NtC A 2646 2648 AA00 .5
############




############
# In this optional second stage, you can turn the hairpin into a GNRA tetraloop.
############
readAtStage 2
# You can upload the provided 5MRC.GNRA.pdb to dnatco.org and see which Nucleotide Conformers (NtC's) are needed to recapitulate the GNRA tetraloop. You should find:
NtC A 2641 2642 AA00 1.5
NtC A 2642 2643 OP03 1.5
NtC A 2643 2644 AA08 1.5
NtC A 2644 2645 AA00 1.5
NtC A 2645 2646 AA05 1.5
# Since we are specifying the conformation of every single residue, we no longer need the non-bonded MD terms:
globalCoulombScaleFactor 0.0
globalVdwScaleFactor 0.0 
# Your structure could be trapped in a local minimum. So let's use the scrubber (potential rescaling) to get out of that:
dutyCycle .9
scrubberPeriod 6
# The  above means forces are turned on 90% of the time, then turned off, with period of 6 ps.
readBlockEnd
############

############
# general parameters
############
# stages
firstStage 1 
lastStage 2
# This is a multiplying factor for the baseInteraction forces:
baseInteractionScaleFactor     200
# Simulation time = reportingInterval * numReportingIntervals :
reportingInterval 3.0
numReportingIntervals  6
temperature 10 
############



#setDefaultMDParameters


readAtStage 3
mobilizer Rigid
alignmentForces A B
readBlockEnd