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About QMMM Free Energy
This document provides instructions for preparing a molecular system for QM/MM simulations by modifying a similar structure from the Protein Data Bank. Specifically, it describes using the VMD molecular modeling program and Tcl scripting to mutate the ligand in the 1X1Z PDB entry of Orotidine 5'-monophosphate decarboxylase from 6-hydroxyuridine-5'-phosphate to orotidine 5'-monophosphate, the natural substrate, and modifying the protein as needed. The goal is to set up a system for studying the enzyme-catalyzed decarboxylation reaction using both classical and quantum mechanical calculations in NAMD.
Detailed Information
| Author: | ['interestingese'] |
|---|---|
| Publication Year: | 2019 |
| Pages: | 13 |
| Language: | English |
| Format: | |
| Price: | FREE |
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