Re: MM/QM with namd

From: jing liang (
Date: Fri Oct 16 2020 - 09:38:48 CDT


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 the
QM 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 why
this line is needed?

After that modification, other two atoms are listed in the Gaussian input
script and I am almost sure that these
are 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 converged
run Gaussian09 didn't print that line and this caused an error. Therefore,
I commented out the lines 236-240. Do you
know 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 comment
would be welcome.

Thank you.

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

> 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.
> Best,
> Marcelo
> On Thu, 15 Oct 2020 at 09:07, Asmi Mahmood <>
> wrote:
>> Hi
>> 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
>> Regards
>> Sent from Yahoo Mail on Android
>> <>

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