I am working on a protein bound to a 77-atom chromophore (BV), for which I do not have optimized ff parameters. To start working with this system I was taking ff parameters from similar structures and restraining the chromophore.
I was using CONS HARM BESTFIT FORCE 200 but changes in DIHE and IMPR were too high (for select angles, changes during a 230 ps md were in the order of 10 degrees, although the stdv was ~ 2). I tried to increase the force to 2000, the situation improved but not enough. As dihedrals and impropers are crucial in our chromophore, I decided to add a restraint on the IC of the chromophore heavy atoms:
cons IC BOND 2000 ANGLE 2000 DIHE 2000 IMPR 2000
cons harm bestfit force 200 sele segid BV end
This means that on some atoms I have multiple restraints. Is this a problem in principle? I am also using SHAKE BONH on the all system, on the chromophore I have then 2 restraints -CONS HARM and CONS IC- and the shake constraint.
As my md simulations keep crashing after warnings of the type:

EPHI: WARNING. bent improper torsion angle is far from minimum for;
IPHI= 36 with deltaPHI= 87.7075 MIN= 3.4400 ATOMS: 4831 4829 4826 4824

(atoms belonging to the chromophore and supposed to be restrained), I start suspecting that IC restraint have not been applied.

Thank you in advance for any comment and suggestion