From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Tue Oct 30 2018 - 12:43:50 CDT
Great, I will go over that material again, thanks! A question about QM region water molecules, all of the atoms in the water molecule would have beta set to 1.0, but I wouldn't need to do anything with the occupancy column correct? They don't need an QM/MM bond defined, right? Thanks!
Kelly L. McGuire
Department of Physiology and Developmental Biology
Brigham Young University
Provo, UT 84602
From: Marcelo C. R. Melo <melomcr_at_gmail.com>
Sent: Tuesday, October 30, 2018 11:15:42 AM
To: NAMD; McGuire, Kelly
Subject: Re: namd-l: QM/MM Error
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 bonds.
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<https://www.ks.uiuc.edu/Research/qmmm/>, and in the tutorials we covered during the workshop, but you will find the "Example 1<https://www.ks.uiuc.edu/Research/qmmm/Examples/Example1.tar.gz>" 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 crdsdsr2_at_illinois.edu<mailto:crdsdsr2_at_illinois.edu> +1 (217) 244-5983 On Mon, 29 Oct 2018 at 00:03, McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> 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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