Dear Amber team and expert users,
I've prepared prmtop/inpcrd files for a metalloprotein-ligand system with
Heme-Fe.
I'm curious regarding the feasibility and usage for QM/MM-MD simulations in
Amber using Gaussian16 as the QM engine.
The Amber24 manual has options for this in section 10.2.6.3. AMBER/Gaussian
on Page 177-178. (
https://ambermd.org/doc12/Amber24.pdf)
However, the namelist variable "basis" doesn't give details on whether one
can use pseudopotentials (ECPs) as in typical QM or QM/MM jobs in
Gaussian16.
If not what would be the best compromise between feasibility/accuracy/speed
for setting up such calculations and would it be possible to simulate TS
states if bonds breaking/forming is all within the QM part of the
calculation?
My question may not be clear or meaningful since I've very basic
understanding of the QM/MM-MD and haven't even tried the Amber tutorial for
the same.
Since I have a descent GPU+CPU setup on HPC, I wanted to try it to further
understand/learn the detailed (science/technical) aspects.
Thus, I am hoping that someone on the Amber team can give some valuable
suggestions, and tips for attempting to setup such complicated QM/MM-MD
simulations and try to simulate the proton transfer step (RC---H---O=FePor)
and possibly estimate the barrier for the same.
Thank you once again for your continued support and valuable suggestions.
Best regards,
Regards,
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Mob. No. +91-7709129400,
Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
https://niperguwahati.ac.in/DOC/profile/dixit.pdf
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
NCBI bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Mon Nov 25 2024 - 03:00:03 PST
