MOLINFO STRUCTURE=ref5.pdb  MOLTYPE=rna
 
#Number of total residues: 2
#Number of biased residues: 2
 
###########################
#### Torsions
###########################
 
#### alpha
 
a2: TORSION ATOMS=@alpha-2 #biased
 
#### beta
 
b2: TORSION ATOMS=@beta-2 #biased
 
#### gamma
 
g1: TORSION ATOMS=@gamma-1 #biased
g2: TORSION ATOMS=@gamma-2 #biased
 

#### epsilon
 
e1: TORSION ATOMS=@epsilon-1 #biased
 
#### zeta
 
z1: TORSION ATOMS=@zeta-1 #biased
 
#### chi
 
c1: TORSION ATOMS=@chi-1 #biased
c2: TORSION ATOMS=@chi-2 #biased
 
###########################
#### Puckering
###########################
 
puck1: PUCKERING ATOMS=@sugar-1  #biased
puck2: PUCKERING ATOMS=@sugar-2  #biased
 
###########################
#### Base COM minimum distances
###########################
 
 
#### Center of Mass
 
WHOLEMOLECULES ENTITY0=@base-1
com1: COM ATOMS=@base-1
WHOLEMOLECULES ENTITY0=@base-2
com2: COM ATOMS=@base-2
 
#### Sort distances
 
 
### Residue1
## Distances between COMs
d1_2: DISTANCE ATOMS=com1,com2
 
## Sorting values of distances
sort1: SORT ARG=d1_2 
## Coordination number between the bases com
co1: COORDINATION R_0=0.4 GROUPA=com1 GROUPB=com2  #biased
 
### Residue2
## Distances between COMs
d2_1: DISTANCE ATOMS=com2,com1
 
## Sorting values of distances
sort2: SORT ARG=d2_1 
## Coordination number between the bases com
co2: COORDINATION R_0=0.4 GROUPA=com2 GROUPB=com1  #biased

####J COUPLINGS###
#Jh3h4_1
n1_1: TORSION ATOMS=10,9,25,26
n1_2: TORSION ATOMS=41,40,56,57
n2_1: TORSION ATOMS=26,25,23,24
n2_2: TORSION ATOMS=57,56,54,55
n3_1: TORSION ATOMS=24,23,6,7
n3_2: TORSION ATOMS=55,54,37,38
n4_1: TORSION ATOMS=7,6,3,4
n4_2: TORSION ATOMS=7,6,3,5
n5_1: TORSION ATOMS=38,37,34,35
n5_2: TORSION ATOMS=38,37,34,36
chi1_1: TORSION ATOMS=10,9,11,12 
chi1_2: TORSION ATOMS=41,40,42,43

x_1: TORSION ATOMS=9,26,27,23
x_2: TORSION ATOMS=40,57,58,54

#(Jh1'-h2')_1/2
j1_1: MATHEVAL ARG=n1_1 FUNC=9.67*cos(x)*cos(x)-2.03*cos(x) PERIODIC=NO
j1_2: MATHEVAL ARG=n1_2 FUNC=9.67*cos(x)*cos(x)-2.03*cos(x) PERIODIC=NO
#(Jh2'-h3')_1/2
j2_1: MATHEVAL ARG=n2_1 FUNC=9.67*cos(x)*cos(x)-2.03*cos(x) PERIODIC=NO
j2_2: MATHEVAL ARG=n2_2 FUNC=9.67*cos(x)*cos(x)-2.03*cos(x) PERIODIC=NO
#(Jh3'-h4')_1/2
j3_1: MATHEVAL ARG=n3_1 FUNC=9.67*cos(x)*cos(x)-2.03*cos(x) PERIODIC=NO
j3_2: MATHEVAL ARG=n3_2 FUNC=9.67*cos(x)*cos(x)-2.03*cos(x) PERIODIC=NO

#(jh4'-h5')_1/2
j4_1: MATHEVAL ARG=n4_1 FUNC=8.313*cos(x)*cos(x)-0.99*cos(x)+0.27*cos(x)*sin(x)+1.373 PERIODIC=NO
j4_2: MATHEVAL ARG=n4_2 FUNC=8.313*cos(x)*cos(x)-0.99*cos(x)+0.27*cos(x)*sin(x)+1.373 PERIODIC=NO

##(jh4'-h5'')_1/2
j5_1: MATHEVAL ARG=n5_1 FUNC=8.313*cos(x)*cos(x)-0.99*cos(x)-4.752*cos(x)*sin(x)+1.373 PERIODIC=NO
j5_2: MATHEVAL ARG=n5_2 FUNC=8.313*cos(x)*cos(x)-0.99*cos(x)-4.752*cos(x)*sin(x)+1.373 PERIODIC=NO


##(jc4-jh')_1/2
j6_1: MATHEVAL ARG=c1 FUNC=3.9*cos(x-(pi/180.0)*70.4)*cos(x-(pi/180.0)*70.4)+1.7*cos(x-(pi/180.0)*70.4)+0.3 PERIODIC=NO
j6_2: MATHEVAL ARG=c2 FUNC=3.9*cos(x-(pi/180.0)*70.4)*cos(x-(pi/180.0)*70.4)+1.7*cos(x-(pi/180.0)*70.4)+0.3 PERIODIC=NO
##(jc8-h1')_1/2
j7_1: MATHEVAL ARG=chi1_1 FUNC=4.8*cos(x+(pi/180.0)*(60.0-66.9))*cos(x+(pi/180.0)*(60.0-66.9))+0.7*cos(x+(pi/180.0)*(60.0-66.9))+0.3 PERIODIC=NO
j7_2: MATHEVAL ARG=chi1_2 FUNC=4.8*cos(x+(pi/180.0)*(60.0-66.9))*cos(x+(pi/180.0)*(60.0-66.9))+0.7*cos(x+(pi/180.0)*(60.0-66.9))+0.3 PERIODIC=NO
##(JC4'-P)_1/2
j11_1: MATHEVAL ARG=e1 FUNC=6.9*cos(x)*cos(x)-3.4*cos(x)+0.7 PERIODIC=NO
j11_2: MATHEVAL ARG=b2 FUNC=6.9*cos(x)*cos(x)-3.4*cos(x)+0.7 PERIODIC=NO

#Jh5'-P
j8: MATHEVAL ARG=b2 FUNC=18.1*cos(x-2.0944)*cos(x-2.0944)-4.8*cos(x-2.0944) PERIODIC=NO

##Jh5''-P
j9: MATHEVAL ARG=b2 FUNC=18.1*cos(x+2.0944)*cos(x+2.0944)-4.8*cos(x+2.0944) PERIODIC=NO

##Jh3'-P
j10: MATHEVAL ARG=e1 FUNC=15.3*cos(x+2.0944)*cos(x+2.0944)-6.1*cos(x+2.0944)+1.6 PERIODIC=NO


#Jc2'-p
j12: MATHEVAL ARG=e1 FUNC=6.9*cos(x-2.0944)*cos(x-2.0944)-3.4*cos(x-2.0944)+0.7 PERIODIC=NO



j1: COMBINE ARG=j1_1,j1_2 PERIODIC=NO
j2: COMBINE ARG=j2_1,j2_2 PERIODIC=NO
j4: COMBINE ARG=j4_1,j4_2 PERIODIC=NO
j5: COMBINE ARG=j5_1,j5_2 PERIODIC=NO
jA3: CONSTANT VALUES=0.0 
jA6: CONSTANT VALUES=0.0
jA7: CONSTANT VALUES=0.0
jC3: COMBINE ARG=j3_1,j3_2 PERIODIC=NO 
jC6: COMBINE ARG=j6_1,j6_2 PERIODIC=NO
jC7: COMBINE ARG=j7_1,j7_2 PERIODIC=NO
