On Mon, Aug 30, 2004 at 10:36:52AM +0900, Han Choe wrote:
> I use the follwoing example to restrain a distance .
>
> SET ATOM_IDS 'OD2:97:' 'NZ:120:'
>
> ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 4.0 0.2
>
> But I don't know how to restrain mainchain and sidechain dihedral angles.
> Would someone explain or post an example script?
ADD_RESTRAINT only works for distances. For other kinds of restraints,
you'll have to write a restraints file out by hand (sorry). See
http://salilab.org/modeller/manual6v2/node98.html for the file format.
An example:
R 3 1 3 11 4 2 0 1 2 3 4 0.3452 0.0134
By reference to the manual, this enforces a Modeller format restraint
(R) of form 3 (harmonic potential) on feature 3 (dihedral angle). The
restraint energy is reported in group 11 (mainchain phi dihedral
restraints). Being a dihedral angle, it acts on 4 atoms, which I've
given here as atoms 1, 2, 3 and 4. Being a harmonic potential, there are
2 parameters, the mean and the standard deviation (both in radians)
which I've given as 0.3452 and 0.0134 respectively.
Once you've created this restraints file, you can add it to the homology
restraints by looking at
http://salilab.org/modeller/FAQ6v2.html#10
Ben Webb, Modeller Caretaker
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