Search

Theoretical and Computational Chemistry

Working Paper

Exploring Coupled Redox and pH Processes with a Force Field-Based Approach: Applications to Five Different Systems

Vinicius Cruzeiro, Gustavo Troiano Feliciano, Adrian Roitberg

Version 1 posted 03 February 2020

466

Downloads

Theoretical and Computational Chemistry

Working Paper

ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution

Chuan Tian, Koushik Kasavajhala, Kellon Belfon, Lauren Raguette, He Huang, Angela Migues, John Bickel, Yuzhang Wang, Jorge Pincay, Qin Wu, Carlos Simmerling

Version 1 posted 17 June 2019

3,092

Downloads

1

Citations

Theoretical and Computational Chemistry

Working Paper

Blinded Prediction of Protein-Ligand Binding Affinity Using Amber Thermodynamic Integration for the 2018 D3R Grand Challenge 4

Junjie Zou, Chuan Tian, Carlos Simmerling

Version 1 posted 24 June 2019

1,111

Downloads

Theoretical and Computational Chemistry

Working Paper

Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation.

Aliza Rubenstein, Kristin Blacklock, Hai Nguyen, David Case, Sagar Khare

Version 2 posted 04 April 2018

1,616

Downloads

Theoretical and Computational Chemistry

Working Paper

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations

Ido Ben-Shalom, Zhixiong Lin, Brian Radak, Charles Lin, Woody Sherman, Michael K. Gilson

Version 1 posted 20 July 2020

599

Downloads

1

Citations

Theoretical and Computational Chemistry

Working Paper

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose…Nucleobase Lone-pair…π Contacts in Nucleic Acids.

Klaudia Mrazikova, Jiri Sponer, Vojtech Mlynsky, Pascal Auffinger, Holger Kruse

Version 1 posted 15 September 2021

289

Downloads

Chemical Engineering and Industrial Chemistry

Working Paper

Molecular Modelling of Ionic Liquids: General Guidelines on Fixed-Charge Force Fields for Balanced Descriptions

Zhaoxi Sun, Zhihao Gong, Lei Zheng, Payam Kalhor, Zhe Huai, Zhirong Liu

Version 2 posted 30 June 2022

532

Downloads

Biological and Medicinal Chemistry

Working Paper

Simulating Chalcogen Bonding Using Molecular Mechanics: A Pseudoatom Approach to Model Ebselen.

Thomas Fellowes, JONATHAN WHITE

Version 2 posted 05 May 2021

691

Downloads

Theoretical and Computational Chemistry

Working Paper

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK

Vinicius Cruzeiro, Madushanka Manathunga, Kenneth M. Merz, Jr., Andreas Goetz

Version 1 posted 16 February 2021

2,222

Downloads

Theoretical and Computational Chemistry

Working Paper

Validation of AMBER/GAFF for Relative Free Energy Calculations

Lin Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.

Version 1 posted 04 February 2019

1,823

Downloads

2

Citations

Refine Search

17 results in amber in Keywords: amber

Exploring Coupled Redox and pH Processes with a Force Field-Based Approach: Applications to Five Different Systems

ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution

Blinded Prediction of Protein-Ligand Binding Affinity Using Amber Thermodynamic Integration for the 2018 D3R Grand Challenge 4

Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation.

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose…Nucleobase Lone-pair…π Contacts in Nucleic Acids.

Molecular Modelling of Ionic Liquids: General Guidelines on Fixed-Charge Force Fields for Balanced Descriptions

Simulating Chalcogen Bonding Using Molecular Mechanics: A Pseudoatom Approach to Model Ebselen.

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK

Validation of AMBER/GAFF for Relative Free Energy Calculations

17 results in Keywords: amber