Adding Static Waters to the Protein Structure

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If you have ordered waters in your structure, DOCK3.7 can use them, but you have to add hydrogens 'manually' using some visualization program and your intuition.

See this tutorial for AMBER minimization:

   http://wiki.docking.org/index.php/Minimize_protein-ligand_complex_with_AMBER

Once this is done, copy the water coordinates into your "rec.pdb" file before blastermaster. Your "rec.pdb" file should have lines that look like this:

ATOM   3662  O   HOH A 508      18.556  19.072  63.314  1.00 44.77           O 
ATOM   3663  H01 HOH A 508      17.624  19.004  63.503  1.00 44.77           H  
ATOM   3664  H02 HOH A 508      18.960  18.206  63.383  1.00 44.77           H

Note the atom naming, it is important to use exactly these names. DO NOT USE "WAT" as residue name.

Once you're done, proceed as normal with protein receptor preparation.

http://i.creativecommons.org/l/by-sa/3.0/88x31.png

This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/ This page is adapted from "DOCK3.7 Documentation" by Ryan G. Coleman. Based on a work at https://sites.google.com/site/dock37wiki/.