I am trying to model a protein with certain distance restraints and
disulphide bonds. I wonder why restraint does not work when I set
disulphide bonds.
What do you mean by "does not work"? Your script looks fine to me.
What can be the
reason that it does not work with S-S restraints. Moreover, Is there a
way to control force constant for harmonic restraints in such cases ?
Technically, you are not adding an S-S restraint - you are telling
Modeller that the two disulfides are bonded, so when it turns on the
CHARMM forcefield you'll get a term in the scoring function that
corresponds to the S-S bond. So if you want to adjust that force
constant (I can't imagine why you'd want to) the way to do it would be
to edit the CHARMM parameter file, modlib/par.lib (in the BOND section,
which is arranged by CHARMM atom type; the two S atoms are type SM, so
you'd be looking around line 291 in Modeller 9.17).