Are AMBER Force Fields and Implicit Solvation Models Additive? A Folding Study with a Balanced Peptide Test Set

2016 ◽  
Vol 12 (11) ◽  
pp. 5631-5642 ◽  
Author(s):  
Melina K. Robinson ◽  
Jacob I. Monroe ◽  
M. Scott Shell
Keyword(s):  
Force Fields ◽  
Implicit Solvation ◽  
Test Set ◽  
Solvation Models ◽  
Amber Force Fields

scholarly journals A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation

2008 ◽  
Vol 112 (22) ◽  
pp. 6878-6886 ◽  
Author(s):  
M. Scott Shell ◽  
Ryan Ritterson ◽  
Ken A. Dill
Keyword(s):  
Force Fields ◽  
Peptide Stability ◽  
Implicit Solvation ◽  
Amber Force Fields

Assessment of AMBER Force Fields for Simulations of ssDNA

2021 ◽  
Vol 17 (2) ◽  
pp. 1208-1217
Author(s):  
Thomas J. Oweida ◽  
Ho Shin Kim ◽  
Johnny M. Donald ◽  
Abhishek Singh ◽  
Yaroslava G. Yingling
Keyword(s):  
Force Fields ◽  
Amber Force Fields

scholarly journals Excited-states of a rhenium carbonyl diimine complex: solvation models, spin–orbit coupling, and vibrational sampling effects

2017 ◽  
Vol 19 (40) ◽  
pp. 27240-27250 ◽  
Author(s):  
Sebastian Mai ◽  
Hugo Gattuso ◽  
Maria Fumanal ◽  
Aurora Muñoz-Losa ◽  
Antonio Monari ◽  
...  
Keyword(s):  
Absorption Spectra ◽  
Excited States ◽  
Orbit Coupling ◽  
Spin Orbit Coupling ◽  
Spin Orbit ◽  
Implicit Solvation ◽  
Td Dft ◽  
Rhenium Carbonyl ◽  
Solvation Models ◽  
P Absorption

Absorption spectra of [Re(CO)3(imidazole)(phenanthroline)]+ were computed using TD-DFT with QM/MM, frozen-density embedding, and implicit solvation models.

Transferability of Local Density-Assisted Implicit Solvation Models for Homogeneous Fluid Mixtures

2019 ◽  
Vol 15 (5) ◽  
pp. 2881-2895 ◽  
Author(s):  
David Rosenberger ◽  
Tanmoy Sanyal ◽  
M. Scott Shell ◽  
Nico F. A. van der Vegt
Keyword(s):  
Local Density ◽  
Implicit Solvation ◽  
Homogeneous Fluid ◽  
Fluid Mixtures ◽  
Solvation Models

Thermodynamics of Helix formation in small peptides of varying lengthin vacuo, implicit solvent and explicit solvent: Comparison between AMBER force fields

2019 ◽  
Vol 18 (03) ◽  
pp. 1950015
Author(s):  
Zhaoxi Sun ◽  
Xiaohui Wang
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Hydrogen Bonds ◽  
Force Fields ◽  
Implicit Solvent ◽  
Conformational Ensemble ◽  
Helix Formation ◽  
Solvent Models ◽  
Explicit Solvent ◽  
Amber Force Fields

Helix formation is of great significance in protein folding. The helix-forming tendencies of amino acids are accumulated along the sequence to determine the helix-forming tendency of peptides. Computer simulation can be used to model this process in atomic details and give structural insights. In the current work, we employ equilibrate-state free energy simulation to systematically study the folding/unfolding thermodynamics of a series of mutated peptides. Two AMBER force fields including AMBER99SB and AMBER14SB are compared. The new 14SB force field uses refitted torsion parameters compared with 99SB and they share the same atomic charge scheme. We find that in vacuo the helix formation is mutation dependent, which reflects the different helix propensities of different amino acids. In general, there are helix formers, helix indifferent groups and helix breakers. The helical structure becomes more favored when the length of the sequence becomes longer, which arises from the formation of additional backbone hydrogen bonds in the lengthened sequence. Therefore, the helix indifferent groups and helix breakers will become helix formers in long sequences. Also, protonation-dependent helix formation is observed for ionizable groups. In 14SB, the helical structures are more stable than in 99SB and differences can be observed in their grouping schemes, especially in the helix indifferent group. In solvents, all mutations are helix indifferent due to protein–solvent interactions. The decrease in the number of backbone hydrogen bonds is the same with the increase in the number of protein–water hydrogen bonds. The 14SB in explicit solvent is able to capture the free energy minima in the helical state while 14SB in implicit solvent, 99SB in explicit solvent and 99SB in implicit solvent cannot. The helix propensities calculated under 14SB agree with the corresponding experimental values, while the 99SB results obviously deviate from the references. Hence, implicit solvent models are unable to correctly describe the thermodynamics even for the simple helix formation in isolated peptides. Well-developed force fields and explicit solvents are needed to correctly describe the protein dynamics. Aside from the free energy, differences in conformational ensemble under different force fields in different solvent models are observed. The numbers of hydrogen bonds formed under different force fields agree and they are mostly determined by the solvent model.

Structures and infrared spectra of calcium phosphate clusters by ab initio methods with implicit solvation models

2018 ◽  
Vol 20 (1) ◽  
pp. 345-356 ◽  
Author(s):  
Tzu-Jen Lin ◽  
Cheng-Chau Chiu
Keyword(s):  
Calcium Phosphate ◽  
Ab Initio ◽  
Infrared Spectra ◽  
Ab Initio Methods ◽  
Implicit Solvation ◽  
Solvation Models ◽  
Stable Structures

We found alternative stable structures of Ca9(PO4)6 other than Posner's cluster in water.

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