ADL: What kind of models use AutoDock in the different stages of docking?

mcmartin at student.matnat.uio.no mcmartin at student.matnat.uio.no
Tue Apr 28 05:12:57 PDT 2009


Hi all, some theoretical questions:

Does autodock use the AMBER force fields to assign the potential
interaction for each grid point when pre-calculating the grids? If not,
what model does it use?

Does it only use the AMBER force fields to assign the non-bonded
interactions between the ligands atoms and the grid points in the 3D box
in the docking procedure itself?

Last, autodock uses the Kollman charges or the Gasteiger charges when
loading a macromolecule in AutoDock tools... are Kollman charges here =
MM2*?

Marcus



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