Re: [AMBER] QM/MM in Amber

From: David A Case <>
Date: Tue, 2 Feb 2021 08:30:39 -0500

On Tue, Feb 02, 2021, Женя Елизарова wrote:
>I am wondering if it is possible to add a link atom between QM and MM parts
>of the system into molecule? I want to split GTP molecule into QM
>(triphosphate) and MM (guanosine) parts. If there is an opportunity, could
>you help me and write any instructions on how i can do it, please?

Technically, you should specify the atoms you want to be "QM", and program
does all the rest of the work. If the system "falls apart", use parmed
to make sure you have a bond between the two parts of the system. Without
more information, it's hard to tell what has happened here.

In the area of unsolicited advice, treating the tri-phosphate as QM sounds
odd: a key part of highly charged groups is their interaction with waters
and ions. For good results, you would almost need to re-parameterize the
phosphate-water and phosphate-ion interactions based on the QM method that
you choose. Are you thinking about something like pulling off the end
phosphate to make a diphosphate?


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Received on Tue Feb 02 2021 - 06:00:03 PST
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