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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.

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Rapid in-silico Battery Electrolyte Electrochemical Reaction Generation using 3T-VASP Multi-Scale Energy Minimization
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Automated conformational energy fitting for force-field development.

Olgun Guvench1, Alexander D MacKerell

  • 1Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn St., HSF II-629, Baltimore, MD 21201, USA.

Journal of Molecular Modeling
|May 7, 2008
PubMed
Summary
This summary is machine-generated.

A new procedure uses Monte Carlo simulated annealing (MCSA) to optimize molecular mechanics force fields. This method refines dihedral and correction map (CMAP) parameters, minimizing energy errors for better molecular simulations.

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Biophysics

Background:

  • Molecular mechanics force fields are crucial for simulating molecular behavior.
  • Accurate parametrization of dihedral and correction map (CMAP) terms is essential for reliable simulations.
  • Existing methods may lack the flexibility to handle complex, multi-dimensional parameter spaces.

Purpose of the Study:

  • To present a general conformational-energy fitting procedure using Monte Carlo simulated annealing (MCSA).
  • To develop an optimized set of dihedral or grid-based correction map (CMAP) parameters for molecular mechanics force fields.
  • To provide a freely available Python tool for dihedral parameter fitting.

Main Methods:

  • Utilizing Monte Carlo simulated annealing (MCSA) to search parameter space.
  • Minimizing the root mean squared error (RMSE) between target and parametrized potential energies.
  • Applying the method to multi-dimensional fitting of cyclohexane, tetrahydropyran, hexopyranose, and polypeptide energetics.

Main Results:

  • The MCSA procedure consistently converges to the same RMSE, regardless of initial parameters.
  • Simultaneous parametrization of multiple dihedral parameters is enabled, accommodating multi-dimensional potential energy scans.
  • Successful application to complex systems, including a 30-dimensional parameter space for hexopyranose.
  • Developed a CMAP parametrization capturing alanine dipeptide and tetrapeptide energetics.

Conclusions:

  • The presented MCSA-based fitting procedure offers a robust and generalizable approach for developing molecular mechanics force fields.
  • The method effectively optimizes dihedral and CMAP parameters, improving the accuracy of molecular simulations.
  • The freely available Python script 'fit_dihedral.py' facilitates wider adoption and application in computational chemistry research.