Connecting Quantum Mechanics to Molecular Dynamics: Generating a Ligand Topology
Poster Number
13B
Format
Poster Presentation
Faculty Mentor Name
Mike McCallum
Faculty Mentor Department
Chemistry
Additional Faculty Mentor Name
Hyun Joo
Abstract/Artist Statement
A topology file provides the physical parameters necessary for Molecular Dynamic (MD) simulations. A topology file needs to be generated from a set of coordinates from Quantum Mechanical (QM) calculations. We used Gaussian to optimize and generate the classical charges for the ligand LDN, which is the first time the topology for this molecule has been calculated. After calculations are finished, rotations around non-chiral atoms can be made to possibly find more stable conformations that could be different than the given structure. Once a minimum is found a force-field topology file can then be constructed. This will be released for use by other scientists as part of the large dictionary of topology files for the CHARMM force-field. This means that other users will be able to use different sections of LDN’s topology for other molecules that have a similar structure. By having a ligand’s topology, we are able to better understand the factor that it’s charge plays into binding. The ability to run a MD simulation also gives us the ability to understand how the ligand possibly binds to the site and how we could improve the manufactured ligand. Having a large library of ligand topologies is very helpful in the field of drug discovery.
Location
DeRosa University Center Ballroom
Start Date
27-4-2018 12:30 PM
End Date
27-4-2018 2:30 PM
Connecting Quantum Mechanics to Molecular Dynamics: Generating a Ligand Topology
DeRosa University Center Ballroom
A topology file provides the physical parameters necessary for Molecular Dynamic (MD) simulations. A topology file needs to be generated from a set of coordinates from Quantum Mechanical (QM) calculations. We used Gaussian to optimize and generate the classical charges for the ligand LDN, which is the first time the topology for this molecule has been calculated. After calculations are finished, rotations around non-chiral atoms can be made to possibly find more stable conformations that could be different than the given structure. Once a minimum is found a force-field topology file can then be constructed. This will be released for use by other scientists as part of the large dictionary of topology files for the CHARMM force-field. This means that other users will be able to use different sections of LDN’s topology for other molecules that have a similar structure. By having a ligand’s topology, we are able to better understand the factor that it’s charge plays into binding. The ability to run a MD simulation also gives us the ability to understand how the ligand possibly binds to the site and how we could improve the manufactured ligand. Having a large library of ligand topologies is very helpful in the field of drug discovery.