Re: [modeller_usage] restraining bonds between het ligand and side chain atoms

[Modeller Caretaker <>]

On 08/03/2009 08:11 PM, Violetta Kivovich wrote:
> I am trying to introduce a restrain which would limit a bond length
> between a zinc and its coordinating side chain atom (N2 of His or O of
> Asn) in my model. I am not sure how to indicate the restraint in a
> script. Can you help?

The "adding additional restraints to the defaults" example is closest to 
what you want to do:
http://salilab.org/modeller/9v7/manual/node27.html

That example builds a set of secondary structure restraints (which you 
don't need), plus a single distance restraint. Let's look at that 
distance restraint more closely:

        rsr.add(forms.gaussian(group=physical.xy_distance,
                               feature=features.distance(at['CA:35'],
                                                         at['CA:40']),
                               mean=10.0, stdev=0.1))

Going from the inside in, features.distance says that the thing we want 
to constrain is a distance in angstroms between two atoms (the C-alpha 
atoms in residues 35 and 40 in this case). Then we say that the form of 
the restraint on that distance should be a Gaussian (harmonic) function 
(forms.gaussian) with a mean of 10A and a standard deviation of 0.1A. 
(The group is not important unless you want to keep track of violations 
of your restraint, or want to scale the scores.) Finally, rsr.add() adds 
the restraint to the list of all restraints on that model.

You can find a list of all the features and forms at:
http://salilab.org/modeller/9v7/manual/node97.html

In your case, if by "limit" you mean you want the bond length to be 
maintained near some known value, you can use something very similar to 
that above. If you mean you want the length to vary freely but not to 
exceed some known upper limit, you can use forms.upper_bound rather than 
forms.gaussian.

Note also that if your interaction really is a "bond" (i.e. distance is 
less than the sum of the radii of the two atoms, or thereabouts) you 
will get a conflict between your distance restraint and Modeller's van 
der Waals (soft sphere or Lennard Jones) interaction, which will try to 
push the two atoms apart. If that is the case, you should exclude this 
pair of atoms from the nonbonded list by adding an excluded pair with 
something like
    rsr.excluded_pairs.append(excluded_atom(at['CA:35'], at['CA:40']))

Finally, note that if the zinc - sidechain interaction already exists in 
the template, Modeller will most likely maintain that interaction in 
your model automatically. See:
http://salilab.org/modeller/9v7/manual/node65.html
The third bullet point on that page may apply in your case.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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