【摘 要】
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A new modification to AMBER force field by incorporating coupled two-dimensional main chain torsion energy has been examined for balanced representation of secondary structures.In this modified AMBER
【机 构】
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State Key Laboratory of Precision Spectroscopy,Department of Physics and Institute of Theoretical an
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A new modification to AMBER force field by incorporating coupled two-dimensional main chain torsion energy has been examined for balanced representation of secondary structures.In this modified AMBER force field(AMBER032D),the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high level quantum mechanical calculations of small peptides in solution.In this work,MD simulations are carried out to study the folding of two model peptides of α-helix and β-hairpin.Our study shows that both α-helix and β-hairpin can successfully fold using AMBER032D force field with the implementation of polarization effect(AMBER032Dp).For comparison,simulations using standard AMBER03 force field with and without polarization,as well as AMBER032D without polarization,failed to fold both α-helix and β-hairpin successfully.These studies strongly suggest that an accurate torsional energy force field is capable of providing a more balanced representation of both helical and extended conformations.Meanwhile the electrostatic polarization effect is indispensable for the growth of secondary structures.
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