[AMBER] How to deal with Dummy atoms of 4-coordinated Zinc in QM/MM

From: Qing Lv <lvqingjiejie.163.com>
Date: Sat, 21 Dec 2019 15:13:44 +0800 (CST)

Hi Colleagues,

I am doing a QM/MM simulation of an enzyme, in which a Zn2+ coordinated with 2 CYM, 1 HIN and 1 GLU. I use the cationic dummy atom (CADA) approach ( https://www.mayo.edu/research/labs/computer-aided-molecular-design/projects/zinc-protein-simulations-using-cationic-dummy-atom-cada-approach ) and all things are okay in the previous MD simulations.
However, I am not sure how to deal with the 4 cationic dummy atoms in QM/MM simulation? The QM method is DFTB3 (built-in Amber18). The Zinc residue contains 5 atoms: Zn, D1, D2, D3, D4. If I include the dummy atoms in QM region, there seem to be totally 5 zinc atoms, as shown in the .out file. But if I do not include the dummy atoms in QM region, Amber automatically adds 4 hydrogens (link atoms) to Zn, which seems incorrect.

BTW: In both cases, I got such SCC convergence errors, but the simulation was able to continue:
 QMMM SCC-DFTB: !!!! ============= WARNING ============= !!!!
 QMMM SCC-DFTB: Convergence could not be achieved in this step.
 QMMM SCC-DFTB: The calculation will continue, but energies and
 QMMM SCC-DFTB: forces for this step will not be accurate.
vlimit exceeded for step 23; vmax = 21.3919

So, how to deal with these dummy atoms in QM/MM simulations? Anyone may help?

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Received on Fri Dec 20 2019 - 23:30:01 PST
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