On 03/23/2010 08:46 AM, Thomas Evangelidis wrote:Right, but all the restraints you mention are atomistic pairwise restraints. You can't restrain two rings, only two atoms.
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.
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.
If yes how can I measure the values (i.e. energy value
for LJ) from the templates?
Ben Webb, Modeller Caretaker
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