Hello everyone,
I have a protein system (complex with a substrate) with a total charge of -9 (the charge of the ligand is -5 and the protein is -4). I want to do some QM/MM calculations using PM6 method in Gaussian.
Here are my questions and any help would be greatly appreciated:
1- I need to know whether I should neutralize the system before running the calculations or not.
2- And if so, can I add counterions manually without using any scripts?
or 3- Do I have to use a specific software for that?
P.S.: I am not interested in using AMBER to add those counterions, since I don't have the AMBER parameters for my ligands.
Thanks a lot in advance.
1. Usually in QM you do not use counter ions, since the require very expensive basis sets and high cutoffs. Instead you simply set the charge of the system to the proper value in order to keep the chemistry correct and stable.
2. You could of course set them by hand, if you really need them, f.i. cause they are structure relevant.
You are performing QM/MM using Gaussian, means you are using ONIOM scheme. I am agree with Norman Geist suggestions. You can add counter ions to neutralize the system but main problem is that in which region will you add counter ions because you are using two entirely different methods. My suggestion is that, Instead of considering total system charge, try to look the QM region as well as MM region charge and add the counter ions manually as per the charge of both region, resulting you can minimize the over polarization of boundary region.
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