Re: MM/QM with namd

From: Asmi Mahmood (
Date: Tue Oct 27 2020 - 04:37:40 CDT

Thanks for the guiding. I studied the tutorial and yes it could help me. But one thing, i tried to download MOPAC from their site and set email for academic license twice but still no reply from them. Its been more than 10 days. Plz guide me now how to download MOPAC without getting license.
One more thing if i would download all the required softwares in windows 10, would it work to calculate MM/QM.

Thanks in advance


    On Friday, 16 October 2020, 10:32:08 pm GMT+5, Marcelo C. R. Melo <> wrote:
 Yes, you are most likely seeing the link atoms added to the QM calculation (even though they are not part of the original system).
I did not work on the Gaussian script, and have never used Gaussian for QM/MM, so I cannot tell the specifics of that calculation.Maybe people here more knowledgeable in Gaussian output could help, or the original author of that script.

On Fri, 16 Oct 2020 at 10:39, jing liang <> wrote:

thank you for the information, I tried already the script:
However, I observed that the resulting input script for Gaussian contains additional lines for other atoms than theQM ones and this caused a problem for Gaussian which crashed because of them. Therefore, I commented out
the line 119. In this way, only the QM atoms are listed in the Gaussian input script. However, I don't know whythis line is needed?
After that modification, other two atoms are listed in the Gaussian input script and I am almost sure that theseare the link atoms, right?  I got the psf and pdb file from the example:
where, I think, that the link atoms have already been set.

Also, there were some lines that seemed to look for the "Self energy" string in the Gaussian log file. In a first convergedrun Gaussian09 didn't print that line and this caused an error. Therefore, I commented out the lines 236-240. Do youknow why this line is required?

Doing all these modifications, NAMD works with Gaussian but I don't know if what I am doing is correct. Any commentwould be welcome.

Thank you.

El jue., 15 oct. 2020 a las 19:03, Marcelo C. R. Melo (<>) escribió:

Hello Jing Liang and Asmi Mahmood,Since you both asked similar questions on the list today, I'll answer both at the same time.
In the website for NAMD QMMM (, under the "Tutorial" heading, you will find a basic tutorial to get you started, which uses QwikMD to setup the QM/MM simulation in its most standard format.For a slightly more advanced approach, there is also an example showing a TCL script that can help you fine tune your QM region selection.Finally, there is an advanced tutorial based on a Jupyter notebook that helps you set up a free energy estimate based on QM/MM calculations.
Of course, in NAMD's user guide you will also find explanations and a complete list of keywords and their functions.
Regarding NAMD-Gaussian simulations, you will be setting the qmSoftware keyword to "custom" and will need to point qmExecPath to your wrapper script (which you seem to have found already). You should adapt that script for your particular case in order to create a Gaussian input file. To make it clear, the qmConfigLine keyword only works with the native interfaces for MOPAC and ORCA, so you won't need to set it.
I would *strongly suggest* starting with a simple simulation using QwikMD, studying the inputs that are created, and then adapting those to your particular case.
On Thu, 15 Oct 2020 at 09:07, Asmi Mahmood <> wrote:

I need to run MM/QM using namd with orca. Is there any available protocol or tutorial available for it. 
Is there any other means to calculate QM for the active site only and MM for the remaining protein in namd. If any better way to do plz suggest

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