On Tue, Oct 4, 2016 at 3:43 AM, Modeller Caretaker modeller-care@salilab.org wrote: > 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.
I mean, in the generated models those restrained atoms (CA of 1 and 169) are far away (>20A) while distance should be somewhere between within 8A. The CA atom of residues 1 and 169 are close enough in the model when function special_patches is commented. However, I am missing a S-S bond without this function. I do not understand why those two CA atoms are >20 in the model when there is restrain set between them:
rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CA:1'], at['CA:269']), mean=4.0, stdev=4.0))
>> 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).
I understand it now. I guessed it incorrectly. I thought MODELLER may be using this information to restraint both Cys residues during the modeling so that they are close enough to form S-S bond.
Thanks, SM
> > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage