Abstract:
Quantum-mechanical/molecular-mechanical (QM/MM) free energy simulations have been shown to be a valuable tool to accurately model chemical processes in bimolecular systems. However, the high computational cost of ab initio QM/MM free energy simulations limits the routine application of the method. This webinar presents a software package QMHub, which is designed to perform ab initio QM/MM simulations for bimolecular systems under periodic boundary conditions. By combining with enhanced sampling, free energy perturbation, and multiple time stepping methods, as well machine learning techniques, QMHub achieved high efficiency and accuracy in modeling several bimolecular systems. At the end of the webinar, a demonstration of using IQmol to build an AMBER system for an enzyme reaction will be presented.
About the presenter:
Xiaoliang Pan graduated with a B.Sc. degree in chemistry from Jilin University in 2006, and received his Ph.D. degree in physical chemistry from Jilin University in 2012. He then moved to the U.S. and did postdoctoral research at the University of Arizona. He currently works as a postdoctoral researcher at the University of Oklahoma focusing on multiscale free energy simulations of enzyme reactions, as well as a consultant for Q-Chem working on extending the QM/MM functionalities in Q-Chem and IQmol.
Hi @shannon.houck
I watched this webinar “Q-Chem Webinar 72: Multiscale free energy simulations of biochemical reactions using QMHub”
I am very happy to see that we can use the latest version of IQmol to build an AMBER system. I want to build an AMBER system for a crystal structure using IQmol. I want to do QM/MM calculations on a crystal using Qchem software.
I downloaded the latest version of IQmol (3.1) for Windows from IQmol Download
But when I go to the calculation option in IQmol top row I want to choose Amber system builder. I couldn’t find this option. There are only three options (qchem setup, job monitor, and edit servers) similar to the previous version of IQmol.
What should I do to incorporate all the options (Edit amber config, amber system builder, and amber input generator) to help me build an AMBER system using IQmol?
Hi Aarzoo, thanks for the question, and apologies for the delayed response! This feature is not yet in the released version of IQmol, and is instead in the IQmol-3 GitHub repository, under the gromacs branch. You’ll have to clone that repository and build IQmol on your own machine in order to use it. I’ll be sure to post an update in this thread whenever the feature is available in the release version.
Thanks @shannon.houck for the update and please let us know whenever the feature is available in the release version. Can you please give a rough idea of when it will be available?