From: mariano spivak (mariano_at_ks.uiuc.edu)
Date: Sat Apr 04 2020 - 11:40:19 CDT
Forwarding this conversation to include namd-l
---------- Forwarded message ---------
From: Mariano Spivak <marspivak_at_gmail.com>
Date: Sat, Apr 4, 2020 at 11:26 AM
Subject: Re: namd-l: fatal error: error in qm-mm bond assignment
To: M. A <matabay2010_at_gmail.com>
It looks like the file does not follow the directions I gave you.
I understand that your proposed simulation is quite complicated and
requires a lot of detail when selecting the QM-MM bonds, for this I suggest
you build the QM/MM simulation from the beginning using VMD to visualize
the atoms you want (check below for help on this).
However, based on the inspection of your qm-input.pdb file, you have other
more basic problems that tells me you are not entirely familiar with the
QM/MM simulations. For example, some of the QM atoms are missing the
Therefore, before attempting your intended QM/MM system, I strongly suggest
you try an easier QM selection, for example only consider QM the ADP
molecule. Once you have this simulation running without errors, you can
start adding QM atoms for the protein in small steps, for example one side
How to use VMD to visualize the selected QM atoms:
(This assumes you are familiar with VMD)
Load your system in VMD, in the TK console: mol new qm-input.pdb
In the Graphics -> Representations menu, you can select your current QM
atoms by writing "beta 1" in "Selected Atoms" space.
You can create multiple Representations with different "Coloring Method" ->
For example, "beta 1 and resname ADP" will select only the ADP molecule
that is QM
If you are interested in adding atoms from the protein side chains near the
ADP, you can visualize the atoms using "protein and same residue as within
4 of resname ADP"
In VMD you can use "Mouse" -> "Label" -> "Atoms" to click on the atoms you
want to signal as QM to get the index (see terminal), then you can use the
TK console to change the beta value of that atom
"[atomselect top "index yourindex"] set beta 1"
If you do this carefully, you can do the same to specify the QM-MM bonds,
using "occupancy" instead of "beta"
The selection can be combined, for example "beta 1 and occupancy 1" will
visualize QM atoms involved in bonds with MM atoms.
Try working from a simple QM region, in small steps adding atoms and
checking the simulation runs without errors.
On Sat, Apr 4, 2020 at 10:32 AM M. A <matabay2010_at_gmail.com> wrote:
> Dear Mariano
> As you told me I corrected occupancy and beta for QM and MM atoms, but
> unfortunately I faced this error again:
> Info: Using the following PDB file for QM parameters: qm-input.pdb
> Info: Number of QM atoms (excluding Dummy atoms): 330
> ERROR: Atoms 831 and 833 are assigned as QM atoms.
> FATAL ERROR: Error in QM-MM bond assignment.
> Whan I checked it I understood these atoms are related to H of Methyl
> group and O of Carboxyl group
> it will be kind of you if you help me to solve it.
> I sent qm-input.pdb file as well.
> best regards
> Maryam Atabay
> Ph.D in Nano Computational Chemistry
> Department of Physics, Sharif University of Technology
Mariano Spivak, Ph.D.
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois.
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