MOLINFO STRUCTURE=helix.pdb

# two alternative ways to get the same result:
# old way (using a center of mass)
# c: CENTER ATOMS=1,2 WEIGHTS=1,0.5
# p: DISTANCE ATOMS=c,3 COMPONENTS
# ps: DISTANCE ATOMS=c,3 SCALED_COMPONENTS
# new way (resetting reference frame)
FIT_TO_TEMPLATE REFERENCE=align.pdb TYPE=SIMPLE
s: CENTER ATOMS=3
p: POSITION ATOM=s
ps: POSITION SCALED_COMPONENTS ATOM=3
# using one or the other should give the same result and same forces


RESTRAINT ARG=p.x AT=0 SLOPE=1
RESTRAINT ARG=ps.a AT=0 SLOPE=1
RESTRAINT ARG=ps.b AT=0 SLOPE=2
RESTRAINT ARG=ps.c AT=0 SLOPE=3

DUMPATOMS ATOMS=@protein FILE=protein.xyz

