From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Thu Oct 15 2020 - 12:02:38 CDT
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.
Best,
Marcelo
On Thu, 15 Oct 2020 at 09:07, Asmi Mahmood <asmi_mahmood_at_remove_yahoo.com>
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
>
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