[Dock-fans] Amberscore after MD

Francesco Pietra chiendarret at gmail.com
Fri Aug 15 12:47:03 PDT 2008


HI:
For a protein and a ligand I carried out rigid docking, flex docking
and amberscore wirh DOCK6. Then, the complex protein-ligand was
embedded in a lipidic membrane for MD simulation with AMBER 10.

At this point, I would like to carry out amberscore again. Is it wise
to do that for the lowest_energy_structure captured from MD
trajectories with ptraj? If so, working out manually the pdb file,
extracting the parts related to the protein and the ligand for
"Prepare" with Chimera.

The alternative (which I tend to disfavor) is the averaged structure
from the MD simulation.

Or is anything better?

Thanks
francesco pietra


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