scholarly journals Automation of the Charmm General Force Field for Drug-Like Molecules

2011 ◽  
Vol 100 (3) ◽  
pp. 611a ◽  
Author(s):  
Kenno Vanommeslaeghe ◽  
Jayeeta Ghosh ◽  
Narendra K. Polani ◽  
Michael Sheetz ◽  
Sudhakar V. Pamidighantam ◽  
...  
Keyword(s):  
2012 ◽  
Vol 33 (31) ◽  
pp. 2451-2468 ◽  
Author(s):  
Wenbo Yu ◽  
Xibing He ◽  
Kenno Vanommeslaeghe ◽  
Alexander D. MacKerell

2019 ◽  
Vol 116 (3) ◽  
pp. 142a ◽  
Author(s):  
Payal Chatterjee ◽  
Esther Heid ◽  
Christian Schröder ◽  
Alexander D. MacKerell
Keyword(s):  

2003 ◽  
Vol 101 (14) ◽  
pp. 2157-2169 ◽  
Author(s):  
H.-C. LI ◽  
C. MCCABE ◽  
S. T. CUI ◽  
P. T. CUMMINGS ◽  
H. D. COCHRAN

2012 ◽  
Vol 208 (1) ◽  
pp. 255-274 ◽  
Author(s):  
Anna Maria Candela ◽  
Alfonso Romero ◽  
Miguel Sánchez
Keyword(s):  

Author(s):  
Yudong Qiu ◽  
Daniel Smith ◽  
Simon Boothroyd ◽  
Hyesu Jang ◽  
Jeffrey Wagner ◽  
...  

We describe the structure and optimization of the Open Force Field 1.0.0 small molecule force field, code-named Parsley. Parsley uses the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism in which parameter types are assigned directly by chemical perception, in contrast to traditional atom type-based approaches. This method provides a natural means to incorporate increasingly diverse chemistry without needlessly increasing force field complexity. In this work, we present essentially a full optimization of the valence parameters in the force field. The optimization was carried out with the ForceBalance tool and was informed by reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These data were computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. Tests of the resulting force field against compounds and data types outside the training set show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields. <br>


2015 ◽  
Vol 108 (2) ◽  
pp. 160a ◽  
Author(s):  
Lei Fang ◽  
Ignacio Soteras Gutiérrez ◽  
Kenno Vanommeslaeghe ◽  
Alexander D. MacKerell
Keyword(s):  

2021 ◽  
Vol 120 (3) ◽  
pp. 77a
Author(s):  
Payal Chatterjee ◽  
Mert Y. Sengul ◽  
Alexander D. MacKerell

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