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 >