The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development

2013 ◽  
Vol 15 (10) ◽  
pp. 3413 ◽  
Author(s):  
Fan Jiang ◽  
Wei Han ◽  
Yun-Dong Wu
Keyword(s):  
Amino Acids ◽  
Force Field ◽  
Field Development ◽  
Force Field Development

Driving Torsion Scans with Wavefront Propagation

2020 ◽  
Author(s):  
Yudong Qiu ◽  
Daniel Smith ◽  
Chaya Stern ◽  
mudong feng ◽  
Lee-Ping Wang
Keyword(s):  
Potential Energy ◽  
Force Field ◽  
Degrees Of Freedom ◽  
Computational Cost ◽  
Initial Guess ◽  
Field Development ◽  
Force Field Development ◽  
Wavefront Propagation ◽  
Open Source Software Package

<div>The parameterization of torsional / dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields.</div><div>Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms.</div><div>To ensure that the sampled molecular configurations are thermodynamically feasible, constrained QM geometry optimizations are typically carried out, which relax the orthogonal degrees of freedom while fixing the target torsion angle(s) on a grid of values.</div><div>However, the quality of results and computational cost are affected by various factors on a non-trivial PES, such as dependence on the chosen scan direction and the lack of efficient approaches to integrate results started from multiple initial guesses.</div><div>In this paper we propose a systematic and versatile workflow called \textit{TorsionDrive} to generate energy-minimized structures on a grid of torsion constraints by means of a recursive wavefront propagation algorithm, which resolves the deficiencies of conventional scanning approaches and generates higher quality QM data for force field development.</div><div>The capabilities of our method are presented for multi-dimensional scans and multiple initial guess structures, and an integration with the MolSSI QCArchive distributed computing ecosystem is described.</div><div>The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes.</div>

Molecular mechanics force-field development for amino acid zwitterions

2003 ◽  
Vol 24 (1) ◽  
pp. 111-128 ◽  
Author(s):  
K. N. Kirschner ◽  
A. H. Lewin ◽  
J. P. Bowen
Keyword(s):  
Amino Acid ◽  
Force Field ◽  
Molecular Mechanics ◽  
Field Development ◽  
Force Field Development
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