From Karl.F.Moschner@urlus.sprint.com  Tue Feb 21 10:37:02 1995

Sounds about right to me, but, if your program doesn't do so already, you 
should first provide a "standard" orientation such as placing the origin at 
the center of mass and orienting the molecule along the principal moment axes 
or dipoles, if you include charges.  But, depending on your code, you may 
still have to consider reversed orientation, i.e., check if x1(a) = x1(b) or 
x1(a) = -x1(b), if the latter, reverse the orientation, ditto for y and z.

Besides exact superposition, quick screens are the total energy, dipole (if 
you include charges), and moments.  For larger molecules, end-to-end or 
selected interatomic distances afford quick checks.  And, if you're checking a 
series of molecules, molecular weight or elemental composition are effective 
screens.

It's suprising that some/many molecular mechanics packages do not 
support/generate "standard" orientations since it would be helpful not only 
for your problem but also as a start for CoMFA alignments.  However, you could 
easily write your own starting from MOPAC or GAMESS subroutines, if you have 
them.  There may also be a program/subroutine available from QCPE which you 
could modify.  A few years ago I had modified the GAMESS subroutine for 
determining the principal moments to generate standard orienetations for 
Tripos "*.mol" files. It was very fast, requiring only a several seconds to 
reorient lysozyme on an SGI 4D/35.  Unfortunately I no longer have the code 
and would be prohibited from redistributing it even if I did.  My original 
interest was to subsequently compute the 3 principal cross-sectional areas, 
and/or solvent cross-sectioanl areas, to try to relate them to diffusivities 
but I didn't get that far.

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