Article ID: 5 - Last Modified: June 6, 2011
If, after a Jaguar QM calculation, I realign the molecule using the Maestro superimpose tools to bring the orientation of the molecule in line with a reference compound, the dipole moment doesn't move with the molecule and so the dipole moment is no longer correct for the displayed structure. Is there a workaround for this (other than aligning molecules before doing the QM calculation)?
In Maestro 9.0 the dipole translates correctly with the molecule, but doesn't rotate to match the new orientation. Our developers are aware of this problem and working to address it.
At the moment, the only option is to pre-align the molecules before performing the QM calculation. Keep in mind that if you don't want Jaguar to move the structure during calculations and want to keep the original "aligned" orientation you need to turn off "Symmetry" in the Jaguar panel, Molecule tab if you are working with symmetrical molecules and do not want the coordinates to change. This should not be a problem if you have asymmetrical drug-like molecules.
*Note that turning off the symmetry can potentially increase calculation time significantly, particularly for large symmetric molecules.
Keywords: Maestro, dipole, Jaguar, QM
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