Re: QM/MM Error

From: Marcelo C. R. Melo (
Date: Tue Oct 30 2018 - 12:15:42 CDT

Hi Kelly,
I believe this and your previous e-mails are connected, but causing
different issues.

QwikMD is intended to be an "easy" and fast way of setting up QM/MM
simulations. For that reason, it will always select all of the amino acid
residues you select, including backbone, not just the side chain.
This way it knows which atoms to select without braking charge groups, and
which classical and QM atoms to select for QM/MM bonds. The error regarding
atoms assigned as MM atoms is most likely due to a mis-assignment of QM/MM

To solve both issues of selecting specific side chains, certain water
molecules, and no lipids from your membrane, you should consider using a
TCL script through VMD. After creating your VMD selections, the script will
define the QM region by setting the beta values for the selected atoms (for
side chains and water molecules, for example), and select QM/MM bonds by
setting the occupancy values of the QM and MM atoms. It is on you to make
sure that no charge groups are broken, as we did hete in Urbana during the
Hands On workshop. The material is available in the QM/MM website
<>, and in the tutorials we covered
during the workshop, but you will find the "Example 1
particularly useful, as it has a TCL script that does more or less what you
want. It is what QwikMD does "behind the scenes", but you can adapt it for
your particular case.
This small "Example 1" material is not in the tutorials, but is in the
website. It is a middle ground between the fast QwikMD based tutorial, and
the advanced Jupyter notebook tutorial.

Hope this helps.

Marcelo Cardoso dos Reis Melo
PhD Candidate
Luthey-Schulten Group
University of Illinois at Urbana-Champaign
+1 (217) 244-5983
On Mon, 29 Oct 2018 at 00:03, McGuire, Kelly <> wrote:
> I have four sidechains in my QM region (channel is a tetramer).  I keep
> getting this error though:
> Info: Number of QM atoms (excluding Dummy atoms): 56
> ERROR: Atoms 171 and 156 are assigned as MM atoms.
> FATAL ERROR: Error in QM-MM bond assignment.
> Those atoms aren't part of the QM region and should be MM atoms.  Why
> would I get this?
> *Kelly L. McGuire*
> *PhD Scholar*
> *Biophysics*
> *Department of Physiology and Developmental Biology*
> *Brigham Young University*
> *LSB 3050*
> *Provo, UT 84602*

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