restraints.txt

# Sample restraint file for QRNA 0.2

# You can impose Watson-Crick base pairs by specifying appropriate chain letters and residue numbers:
BASEPAIR   B/1   A/32   
BASEPAIR   B/2   A/31   
BASEPAIR   B/3   A/30   
# ...etc. Any non-WC base pairs will be rejected!

# You can also specify distance restraints for pairs of atoms:
DISTANCE   A/3/C4'   B/4/C3'    3    4    50
DISTANCE   A/4/C2'   B/5/O3'    4    4    100
DISTANCE   A/5/C1'   B/6/H2'    5.5  3.5  100
# ...etc. The meaning of numbers is as follows: 
# spring length = average of the first two [in Angstroms]
# spring force constant = the third number

# In this example: DISTANCE   A/3/C4'   B/4/C3'    3    4    50
# we have pair of atoms (C4' from residue 3. in chain A  &  C3' from residue 4. in chain B)
# bound by a spring of rest length of 3.5 A and force constant of 50 kcal/mol/A^2.
# In case of: DISTANCE   A/4/C2'   B/5/O3'    4    4    100
# we have pair of atoms (C2' from residue 4. in chain A  &  O3' from residue 5. in chain B)
# bound by a spring of rest length of 4 A and force constant of 100 kcal/mol/A^2.