Project ID: plumID:20.029
Source: E2F1-DP1_PLUMED-NEST/SINGLE_REPLICA/plumed-restraints.dat

# RESTRAIN DNA

A466_T437_H1: DISTANCE NOPBC ATOMS=@N6-466,@O4-437 
A466_T437_H2: DISTANCE NOPBC ATOMS=@N1-466,@N3-437 

G452_C451_H1: DISTANCE NOPBC ATOMS=@N2-452,@O2-451 
G452_C451_H2: DISTANCE NOPBC ATOMS=@N1-452,@N3-451 
G452_C451_H3: DISTANCE NOPBC ATOMS=@O6-452,@N4-451 

RESTRAINT ARG=A466_T437_H1,A466_T437_H2,G452_C451_H1,G452_C451_H2,G452_C451_H3 AT=0.29,0.29,0.29,0.29,0.29  KAPPA=1000.0,1000.0,1000.0,1000.0,1000.0 LABEL=RESTRAINT_DNA


# RESTRAIN ARGININE HBONDS
# see Genes Dev. 1999 Mar 15; 13(6): 666–674 [Reference paper for pdb: 1cf7]. Figure 4.
# consider common recognition sequence: C442-C445/G458-G462

R46_DG458: DISTANCE NOPBC ATOMS=@NE-46,@O6-458
R47_DG444: DISTANCE NOPBC ATOMS=@NH2-47,@O6-444
R250_DG442: DISTANCE NOPBC ATOMS=@NE-250,@O6-442
R251_DG460: DISTANCE NOPBC ATOMS=@NH2-251,@O6-460

RESTRAINT ARG=R46_DG458,R47_DG444,R250_DG442,R251_DG460 AT=0.29,0.29,0.29,0.29  KAPPA=1000.0,1000.0,1000.0,1000.0 LABEL=RESTRAINT_ARG



# PRINT
PRINT ARG=RESTRAINT_DNA.bias,RESTRAINT_ARG.bias STRIDE=2000 FILE=RESTRAINTS
PRINT ARG=A466_T437_H1,A466_T437_H2,G452_C451_H1,G452_C451_H2,G452_C451_H3,R46_DG458,R47_DG444,R250_DG442,R251_DG460 STRIDE=2000 FILE=HBONDS