I'm doing a single frame QM/MM calculation with Amber 2016 just to easily
define the QM region for a subsequent QM calculation with ORCA. No dynamics
are being performed.
Once I am done with the ORCA calculation, I wish to superimpose the results
of that calculation (i.e. surface information) on the total system (one that
includes both the QM and MM atoms). However, I cannot figure out how to get
the coordinate system of the QM calculation properly superimposed on the
total system. It appears the QM atoms have been relocated through some
geometric transformation when Amber generates the QM/MM files.
How do I retain the original coordinates of the QM section prior to Amber
cutting it out of the entire system for QM/MM setup? I could find no
discussion about this in the manual nor in the mailing list.
Thanks
Jim Kress
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Received on Tue Apr 24 2018 - 12:00:02 PDT
