Re: [AMBER] Amino Acid Residues in QM/MM Simulation

From: Gustavo Seabra <>
Date: Tue, 24 May 2016 16:00:44 -0300

The charge of a QM system is defined by: [(number of protons) - (number of electrons)]. When atoms are added to the QM zone, they are considered neutral, that is, by default, the charge on the QM system is zero. If you want it to have a different charge, you have to tell amber.

Look for the ‘qmcharge’ keyword.

Gustavo Seabra.

> Em 23 de mai de 2016, à(s) 23:25, Nisler, Collin R. <> escreveu:
> Hello, I had a question regarding the modeling of amino acids in a QM/MM simulation. If I am including, say, the carbonyl (last two carbons and oxygens) of a glutamate residue in the QM portion, would this add -1 to the charge of the QM system? So if I had, say, four such glutamates and a calcium total in the QM region, would the total charge be -2? Thanks very much.
> Collin Nisler
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Received on Tue May 24 2016 - 12:30:02 PDT
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