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Molecular parameters were set for maximum energy minimization and Amber12 liquid state.
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However, the model with the highest packing score was selected for full energy minimization (MOE packing score is −2.5478).
The local-minimum curve for the energy minimization is identified through appropriate selection of a starting surface with two tethers.
The TNCG minimization method was used for the energy minimization of structures generated by conformational search (35).
For FlexX energy minimization was performed using the tripos force field with a distance gradient algorithm with convergence criterion of 0.05 KCal/(mol Å) and maximum 1000 interactions, respectively.
This polynomial provides the initial values for the energy minimization process.
GROMACS parameters for performing energy minimization and molecular dynamics using GROMACS-4.6.5.
In this step the binary files for the energy minimization step are prepared.
AMBER parameters for performing energy minimization and molecular dynamics using AMBER11.
Subsequently, the conjugated gradient algorithm was applied for further energy minimization until an energy gradient of 42 KJ/mol.nm.nm
Subsequently, the conjugate-gradients algorithm was applied for further energy minimization until an energy gradient fell to 42 KJ/mol.nm.nm
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