Dear Abhishek,
If you are using semiempirical QM or DFTB, you can print Mulliken charges during the QM/MM MD simulation or geometry optimization. If you use an external QM code, you have to perform some sort of population analysis (e.g. NBO or QTAIM) on relevant snapshots. For this purpose you can modify the input files that the sander QM/MM interface writes when executing the external QM code (e.g. gau_job.inp for Gaussian etc).
Whether a given popoulation or charge analysis is meaningful to describe the charge on part of your QM region (e.g. nucleophile) is a different question. You will find many examples in the literature that can help making a good decision.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu<mailto:agoetz.sdsc.edu>
Web: www.awgoetz.de<http://www.awgoetz.de>
On Apr 25, 2018, at 8:38 AM, Thakur, Abhishek <axt651.miami.edu<mailto:axt651.miami.edu>> wrote:
Hi everyone,
I have done a QM/MM simulation for a reaction. Now after running the simulation and getting a transition state (TS) I want to know what is the charge associated with my nucleophile at the TS.
I have tried converting *.rst file to mol2 for the TS and final step and at both step I can find the same charge.
Is there any way that I can exactly get the charge of my TS nucleophile?
Any suggestion will be highly appreciated.
with regards,
-Abhishek
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Received on Wed Apr 25 2018 - 13:00:03 PDT
