On Tue, Apr 24, 2018, James Kress wrote:
> 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.
I'm having trouble understanding where the problem lies. Here's my view
of how Amber handles coordinates in QM/MM:
1. You start with a structure of the whole system, maybe from xray,
maybe from model building.
2. Set up in Amber, and indicate which atoms belong to the quantum
region. This shouldn't change any coordinates; (use "set default
nocenter on" if your full system is a periodic one.)
3. Amber creates an input file of just the quantum atoms (plus link
atoms.) I think the coordinates in this file are just the ones in the full
structure (from step 1).
4. Orca calculates forces, but doesn't modify the coordinates.
These steps don't mesh well with your statement that "QM atoms have been
relocated ...when Amber generates the QM/MM files", but I'm not sure
exactly what you are referring to. Can you give more specifics about
the stage where the QM atoms are getting in the "wrong" place?
....dac
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Received on Tue Apr 24 2018 - 18:30:03 PDT
