From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Fri Oct 16 2020 - 11:37:33 CDT
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 <jingliang2015_at_gmail.com> 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 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 (<melomcr_at_gmail.com>)
>> 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 (http://www.ks.uiuc.edu/Research/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 <asmi_mahmood_at_remove_yahoo.com>
>>> 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
>>> Sent from Yahoo Mail on Android
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