Hi everyone,
I recently used the amber/orca interface to run extensive qm/mm simulations of a substrate in a cyp450 system. I would like to optimize the TS to verify that I have a negative frequency via some frequency calculations. I want to know if I'm doing this the "right" way.
I extracted a frame from the peak of my PMF curve, I am running a restrained qm/mm minimization (first 10000 cycles of the whole system using standard SD, 1000 cycles using XTB2 applied to my qm region and using xmin, then 100 cycles of b97-3c using xmin on the qm region again). The pointcharge file generated from the qm/mm calc is being used as input for the frequency calculations when I run orca alone. Right after the minimization, I run the frequency calc however, while the largest imaginary mode is the movement I am looking for, there are other tinier imaginary frequencies (around 7) for that select frame. Is there a better way to do this? When I extract the coordinates of my qm region and do a restrained optimization alone in orca, while scf calculations converge, the optimization does not. I've tried a large combination of restraints (holding point atoms, following the restrained heme example in the manual) but still lack of geometry convergence.
Ultimately, I would like to get the TS, confirm a singular imaginary mode, then run a homo-lumo analysis. Thanks!
Sincerely,
Peter Ramdhan
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Received on Sun Mar 15 2026 - 15:00:03 PDT
