Re: [modeller_usage] special restrains for aromatic packing interactions
Is it possible to set the distance cutoff between a given atom of the protein and a subset of atoms in the ligand? E.g. in some crystal structures OG1 of a THR forms an H-bond with O1A of ATP, whereas in others with O2A. In that case can I force Modeller to keep (THR44:OG1 - ATP266:O1A <= 3.5+-0.1) OR (THR44:OG1 - ATP266:O2A <= 3.5+-0.1) ?
2010/3/24 Modeller Caretaker modeller-care@salilab.org
> On 03/23/2010 08:46 AM, Thomas Evangelidis wrote: > >> Since the phosphate groups of ATP are forced to lie within 3.5 A. from >> the binding site residues, the Tyrosine ring will be in close proximity >> to the Adenine ring. So I was thinking about adding a Coulomb or LJ or >> SHPERE restraint including only the adenine and tyrosine rings. >> > > Right, but all the restraints you mention are atomistic pairwise > restraints. You can't restrain two rings, only two atoms. > > > If yes how can I measure the values (i.e. energy value >> for LJ) from the templates? >> > > You can measure the template distance in any reasonable PDB viewer, such as > Chimera. Then I'd suggest you just use simple Modeller harmonic pairwise > distance restraints with a mean corresponding to the measured distance, and > tweak the standard deviation until things look right. The reason I suggest > harmonic rather than Coulomb or LJ terms is that unless you're > super-confident the form of the potential is inverse square or 6-12, those > mathematical forms don't make sense. And there's no way you'd be able to > accurately parameterize either interaction short of doing a lot of high > basis set QM calculations. So you're probably better off with a simple > harmonic. > > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >
On 3/24/10 10:36 AM, Thomas Evangelidis wrote: > Is it possible to set the distance cutoff between a given atom of the > protein and a subset of atoms in the ligand?
Sure, you can create a pseudoatom which is some function of the subset, e.g. the gravity center, and then create a distance restraint between the given atom and your newly-created pseudoatom. One example is at http://salilab.org/modeller/wiki/Restraints%20on%20pseudo%20atoms
> E.g. in some crystal > structures OG1 of a THR forms an H-bond with O1A of ATP, whereas in > others with O2A. In that case can I force Modeller to keep (THR44:OG1 - > ATP266:O1A <= 3.5+-0.1) OR (THR44:OG1 - ATP266:O2A <= 3.5+-0.1) ?
You could use features.minimal_distance for this rather than the regular features.distance: http://salilab.org/modeller/9v7/manual/node97.html#SECTION001031200000000000...
Ben Webb, Modeller Caretaker
Thanks, I did what you said and the ligand fits beautifully into the cavity. Just out of curiosity, does automodel.nonstd_restraints() apply only to BLK residues? I tried to override this function to build models with ATP but Modeller always seems to define its own restraints. Do I always have to do that trick with moving the ligand far from the protein, as described in the advanced tutorial?
On 03/26/2010 09:07 PM, Thomas Evangelidis wrote: > Thanks, I did what you said and the ligand fits beautifully into the > cavity. Just out of curiosity, does automodel.nonstd_restraints() apply > only to BLK residues? I tried to override this function to build models > with ATP but Modeller always seems to define its own restraints. Do I > always have to do that trick with moving the ligand far from the > protein, as described in the advanced tutorial?
nonstd_restraints() builds restraints on all HETATM residues: http://salilab.org/modeller/9v7/manual/node65.html
If you simply override it to do nothing (e.g. define the method to simply return, or 'pass') then Modeller will not build any of those restraints.
Note that if you do the "move the ligand far away" trick then Modeller will not build any protein-ligand restraints, but it will still build intra- and inter-residue ligand restraints.
Ben Webb, Modeller Caretaker
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Thomas Evangelidis