This should be fine, provided that you really want the mean to be -1
radians, and that this is within the 'special_restraints' routine or
similar: http://salilab.org/modeller/manual/node32.html
Now when I run modeller with such restraints, in the finally obtained
models, I dont see these exact values of restraints,
which we mentioned explicitly, taken in by the model. Why this is so?
The values of these mentioned dihedral restraints in
the modelled models are far from the prescribed values.
You should check the log file to make sure the restraint is actually
there, and the end of the .rsr file.
Now as I said above that I am giving 15deg as std. deviation,but when I
use smaller values like 5deg or so, the program is
getting failed, it seems that it is getting difficult for it to optimise
the system, with smaller values of std. deviation.
Last but not least, what I tried or trying is that creating the gaps in
this section of 5 residues, where I am imposing
backbone dihedrals, so that MODELLER doesnt find any equivalent residues
in that position in templates and probably reduces
the number of restraints, and in that case I may be able to impose my
restraints well enough for these five residues, but
still results doesnt seems to go hand in hand. Any comments in this
concern also will be helpful.
If you actually are applying the restraint, it is probably being
violated because it clashes with an existing restraint. Modeller will
apply dihedral restraints to your system regardless of whether homology
information is available (if unaligned, it will just use CHARMM
parameters). Therefore you should remove the existing restraints first:
see http://salilab.org/modeller/FAQ.html#4 and the 'cispeptide' script
in modlib/modeller/scripts/cispeptide.py (or the TOP equivalent in
bin/__cispeptide.top) for an example.