Molecular Modeling of Bifunctional Chelate Peptide Conjugates. 1. Copper and Indium Parameters for the AMBER Force Field

2001 ◽  
Vol 40 (20) ◽  
pp. 5223-5230 ◽  
Author(s):  
David E. Reichert ◽  
Per-Ola Norrby ◽  
Michael J. Welch
Keyword(s):  
Molecular Modeling ◽  
Force Field ◽  
Peptide Conjugates ◽  
Amber Force Field

Membrane Protein Simulations Using AMBER Force Field and Berger Lipid Parameters

2012 ◽  
Vol 8 (3) ◽  
pp. 948-958 ◽  
Author(s):  
Arnau Cordomí ◽  
Gianluigi Caltabiano ◽  
Leonardo Pardo
Keyword(s):  
Membrane Protein ◽  
Force Field ◽  
Amber Force Field ◽  
Lipid Parameters

VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems

2016 ◽  
Vol 56 (4) ◽  
pp. 811-818 ◽  
Author(s):  
Suqing Zheng ◽  
Qing Tang ◽  
Jian He ◽  
Shiyu Du ◽  
Shaofang Xu ◽  
...  
Keyword(s):  
Force Field ◽  
Amber Force Field ◽  
Molecular Systems ◽  
Force Field Parameters

scholarly journals IM-UFF: Extending the universal force field for interactive molecular modeling

2017 ◽  
Vol 77 ◽  
pp. 350-362 ◽  
Author(s):  
Léonard Jaillet ◽  
Svetlana Artemova ◽  
Stephane Redon
Keyword(s):  
Molecular Modeling ◽  
Force Field ◽  
Universal Force Field

scholarly journals Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

2020 ◽  
Vol 76 (1) ◽  
pp. 51-62 ◽  
Author(s):  
Nigel W. Moriarty ◽  
Pawel A. Janowski ◽  
Jason M. Swails ◽  
Hai Nguyen ◽  
Jane S. Richardson ◽  
...  
Keyword(s):  
Force Field ◽  
Active Sites ◽  
Protein Structures ◽  
Target Function ◽  
Real Space ◽  
Model Quality ◽  
Nonbonded Interactions ◽  
Amber Force Field ◽  
Quantum Mechanical Representation ◽  
Improved Model

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.

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

Soft Matter ◽  
2012 ◽  
Vol 8 (37) ◽  
pp. 9617 ◽  
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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