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

posted @ 2011-01-10 22:58  greencolor  阅读(174)  评论(0)  编辑  收藏  举报