Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard–Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing.

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GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

Soft Matter ◽

10.1039/c2sm26007g ◽

2012 ◽

Vol 8 (37) ◽

pp. 9617 ◽

Cited By ~ 134

Author(s):

Callum J. Dickson ◽

Lula Rosso ◽

Robin M. Betz ◽

Ross C. Walker ◽

Ian R. Gould

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Force Field ◽

Dynamics Simulation ◽

Amber Force Field

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Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field

Journal of Molecular Modeling ◽

10.1007/s00894-018-3720-x ◽

2018 ◽

Vol 24 (7) ◽

Cited By ~ 1

Author(s):

Slawomir S. Stachura ◽

Chris J. Malajczuk ◽

Ricardo L. Mancera

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Water Mixture ◽

Amber Force Field ◽

Dynamics Simulations

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Plural Origins of Molecular Homochirality in Our Biota Part II. The Relative Stabilities of Homochiral and Mixed Oligoribotides and Peptides

Zeitschrift für Naturforschung C ◽

10.1515/znc-1997-1-216 ◽

1997 ◽

Vol 52 (1-2) ◽

pp. 89-96 ◽

Cited By ~ 6

Author(s):

Thereza Amélia Soares ◽

Roberto Dias Lins ◽

Ricardo Longo ◽

Richard Garratt ◽

Ricardo Ferreira

Keyword(s):

Molecular Dynamics ◽

Amino Acid ◽

Force Field ◽

Molecular Mechanics ◽

Computer Simulations ◽

The Other ◽

Amino Acid Residues ◽

Relative Stabilities ◽

Amber Force Field ◽

Cross Inhibition

Abstract By computer simulations -molecular mechanics and molecular dynamics with the amber force field (Weiner et al., (1986), J. Comp. Chem. 7, 2 30-252) -we have determined the stabilities of oligoribotide strands built with ᴅ -and ʟ-riboses, and of peptide chains with ᴅ -and ʟ-amino acid residues. In particular, complementary double-chains of oligoribotides were studied, since they are an important feature of the growing mechanism of modern nucleic acids. Peptide chains on the other hand, grow without need of a template. We found that mixed oligoribotides are less stable than homochiral ones, and that this chiral effect is less noticeable in peptide chains. The results support the interpretation that ʟ-riboses act as terminators to the template-assisted growth of oligo-r-Gᴅ (enantiomeric cross-inhibition; Joyce et al., (1987), Proc. Natl. Acad. Sci. USA 84, 4398-4402). Based on this effect, a chemical pathway is proposed which could, under assumed prebiotic conditions, bypass the hindrance of homochiral growth.

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Molecular Dynamics Simulations of CO2Molecules in ZIF-11 Using Refined AMBER Force Field

Journal of Chemistry ◽

10.1155/2013/415027 ◽

2013 ◽

Vol 2013 ◽

pp. 1-10 ◽

Cited By ~ 3

Author(s):

W. Wongsinlatam ◽

T. Remsungnen

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Distribution Functions ◽

Binding Energies ◽

Hydrogen Atoms ◽

Amber Force Field ◽

Bonding Parameters ◽

Flexible Framework ◽

Dynamics Simulations

Nonbonding parameters of AMBER force field have been refined based onab initiobinding energies of CO2–[C7H5N2]−complexes. The energy and geometry scaling factors are obtained to be 1.2 and 0.9 forεandσparameters, respectively. Molecular dynamics simulations of CO2molecules in rigid framework ZIF-11, have then been performed using original AMBER parameters (SIM I) and refined parameters (SIM II), respectively. The site-site radial distribution functions and the molecular distribution plots simulations indicate that all hydrogen atoms are favored binding site of CO2molecules. One slight but notable difference is that CO2molecules are mostly located around and closer to hydrogen atom of imidazolate ring in SIM II than those found in SIM I. The Zn-Zn and Zn-N RDFs in free flexible framework simulation (SIM III) show validity of adapting AMBER bonding parameters. Due to the limitations of computing resources and times in this study, the results of flexible framework simulation using refined nonbonding AMBER parameters (SIM IV) are not much different from those obtained in SIM II.

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