The Sigma MD Program and a Generic Interface Applicable to Multi-Functional Programs with Complex, Hierarchical Command Structure

Mann, Geoff; Yun, R. H.; Nyland, Lars; Prins, Jan F.; Board, John A.; Hermans, Jan

doi:10.1007/978-3-642-56080-4_6

Cited by 22 publications

(19 citation statements)

References 29 publications

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“…Finally, the free energy contributions from zero-point energy and thermodynamic vibration were estimated by frequency analysis using the GAUSSIAN03 program. 67 The MD simulations were carried out with the program SIGMA, 68,69 while the QM calculations were performed with GAUSSIAN03. 67 The electrostatic potential fit charges of QM subsystem were obtained with our recently developed method, 70 which improves the numerical stability of the charges on the atoms in the QM region.…”

Section: Computational Detailsmentioning

confidence: 99%

Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

Zhang

et al. 2009

The Journal of Chemical Physics

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A quantum mechanical/molecular mechanical minimum free energy path ͑QM/MM-MFEP͒ method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics ͑MD͒ sampling is only carried out with the QM subsystem fixed. It thus avoids "on-the-fly" QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

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Section: Computational Detailsmentioning

confidence: 99%

Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

Zhang

et al. 2009

The Journal of Chemical Physics

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“…Force fields and molecular parameters for AQP were adapted from those used for ATP. Molecular dynamics simulations for TrpRS monomers were performed with the program SIGMA (Mann et al, 2002), by using the CHARMM27 force field. Snapshots were saved every 400 fs.…”

Section: Experimental Procedures MD Trajectoriesmentioning

confidence: 99%

A Conformational Transition State Accompanies Tryptophan Activation by B. stearothermophilus Tryptophanyl-tRNA Synthetase

Kapustina

Weinreb

et al. 2007

Structure

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B. stearothermophilus tryptophanyl-tRNA synthetase catalysis proceeds via high-energy protein conformations. Unliganded MD trajectories of the pretransition-state complex with Mg(2+)ATP and the (post) transition-state analog complex with adenosine tetraphosphate relax rapidly in opposite directions, the former regressing, the latter progressing along the structural reaction coordinate. The two crystal structures (rmsd 0.7 A) therefore lie on opposite sides of a conformational free-energy maximum as the chemical transition state forms. SNAPP analysis illustrates the complexity of the associated long-range conformational coupling. Switching interactions in four nonpolar core regions are locally isoenergetic throughout the transition. Different configurations, however, propagate their effects to unfavorable, longer-range interactions at the molecular surface. Designed mutation shows that switching interactions enhance the rate, perhaps by destabilizing the ground state immediately before the transition state and limiting nonproductive diffusion before and after the chemical transition state, thereby reducing the activation entropy. This paradigm may apply broadly to energy-transducing enzymes.

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“…Molecular dynamics simulations for TrpRS monomers were performed with the program SIGMA, 38 using the CHARMM27 force field, according to the following protocol.…”

Section: Initial Structures For Simulationsmentioning

confidence: 99%

Computational Studies of Tryptophanyl-tRNA Synthetase: Activation of ATP by Induced-Fit

Kapustina

Carter

2006

Journal of Molecular Biology

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The Sigma MD Program and a Generic Interface Applicable to Multi-Functional Programs with Complex, Hierarchical Command Structure

Cited by 22 publications

References 29 publications

Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

A Conformational Transition State Accompanies Tryptophan Activation by B. stearothermophilus Tryptophanyl-tRNA Synthetase

Computational Studies of Tryptophanyl-tRNA Synthetase: Activation of ATP by Induced-Fit

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