On 10/3/16 1:47 AM, Sushil Mishra wrote: > 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).
Ben Webb, Modeller Caretaker