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A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry
Arghya Chakravorty1, Emilio Gallicchio2, Emil Alexov1
1Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634.
A new grid-based method accurately calculates molecular volume and surface area using a Gaussian atom model. This approach enhances molecular modeling, particularly for free energy calculations in computational chemistry.
Area of Science:
- Computational chemistry
- Molecular modeling
- Biophysics
Background:
- Molecular volume (MV) and surface area (MSA) are critical for calculating nonpolar free energy components.
- Accurate computation of MV and MSA is essential for molecular simulations.
Purpose of the Study:
- To present a novel grid-based method for computing molecular volume and surface area.
- To integrate this method with existing computational chemistry packages like Delphi for Poisson-Boltzmann equation (PBE) solving.
Main Methods:
- A grid-based approach combined with a Gaussian atom model to identify overlapping atomic volumes.
- Construction of a rooted tree using a depth-first method for volume and surface area calculation.
- Utilizing formulations from Grant and Pickup (J. Phys Chem, 1995).
Main Results:
- Demonstrated time efficiency of the novel method.
- Validated performance concerning grid resolution, solute positioning, and overlap identification accuracy.
- Explored the physical meaningfulness of the Gaussian model.
Conclusions:
- The developed method provides a physically meaningful, fast, and robust tool for molecular modeling.
- Future integration with Delphi aims to enhance MM/PBSA free energy calculations.
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