Adding Static Waters to the Protein Structure
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:
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.
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/.