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  • Amber

    Information that all the simulation programs need:

      1. Cartesian coordinates for each atom in the system.

      2. "Topology": connectivity, atom names, atom types, residue names, and charges.This information
          comes from the database, which is found in the amber10/dat/leap/prep directory.

      3. Force field: Parameters for all of the bonds, angles, dihedrals, and atom types in the system.
          The standard parameters for several force fields are found in the amber10/dat/leap/parm
     

    Preparatory programs

       LEaP

       ANTECHAMBER

    Simulation programs

       SANDER (Simulated Annealing with NMRDerived Energy Restraints)

       PMEMD

    Analysis programs

       PTRAJ

       MM-PBSA

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  • 原文地址:https://www.cnblogs.com/greencolor/p/1932414.html
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