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Example sentences for: waals

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The van der Waals interactions were truncated at a distance of 12 Å. The simulations were repeated with five different starting seeds.
The van der Waals, bond, angle, dihedral, and improper dihedral parameters for all the ligands were adopted from the Hetero-compound Information Centre-Uppsala HIC-Up http://xray.bmc.uu.se/hicup [ 55 ] . The water molecule under the flaps present in all complexes was included in all steps throughout this study except for 1hvr, where the structural water was removed in the preparation of the protease to be docked with the ligand (the ligand of 1hvr, which is a urea-based inhibitor, does not bind a water molecule in this position).
The flexible ligand was docked into a combination of five potential map representations of the RAR-α ligand binding pocket, which account for two Van der Waals boundaries, hydrophobicity, electrostatics and hydrogen bonding profiles [ 20, 27].
The calculated Van der Waals repulsions with alpha4-beta2 and alpha3-beta2 nAChRs remain small, and within the accuracy limit of Van der Waals energy prediction (the otherwise negligible displacement of an atom by a tenth of an Angstrom may result in several kcal/mol energy difference).
Energy terms included Van der Waals, electrostatic, hydrogen bond, and torsion terms [ 10 ] .