Adding Static Waters to the Protein Structure - Revision history

Rstein at 19:02, 12 April 2019

2019-04-12T19:02:58Z

← Older revision		Revision as of 19:02, 12 April 2019
Line 5:		Line 5:
	http://wiki.docking.org/index.php/Minimize_protein-ligand_complex_with_AMBER		http://wiki.docking.org/index.php/Minimize_protein-ligand_complex_with_AMBER

	Once this is done, ~~make sure~~ your ~~PDB~~ file ~~looks~~ like this:		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 3662 O HOH A 508 18.556 19.072 63.314 1.00 44.77 O

Rstein at 19:00, 12 April 2019

2019-04-12T19:00:58Z

← Older revision		Revision as of 19:00, 12 April 2019
Line 1:		Line 1:
	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.		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
			See this tutorial for AMBER minimization:

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

	Once this is done, make sure your PDB file looks like this:		Once this is done, make sure your PDB file looks like this:

Rstein at 19:00, 12 April 2019

2019-04-12T19:00:45Z

← Older revision		Revision as of 19:00, 12 April 2019
Line 1:		Line 1:
	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. Once this is done, make sure your PDB file looks like this:		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, make sure your PDB file looks like this:

	ATOM 3662 O HOH A 508 18.556 19.072 63.314 1.00 44.77 O		ATOM 3662 O HOH A 508 18.556 19.072 63.314 1.00 44.77 O
Line 5:		Line 8:
	ATOM 3664 H02 HOH A 508 18.960 18.206 63.383 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. Once you're done, proceed as normal with protein receptor preparation.		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.

	{{Template:CC-BY-SA-30}}		{{Template:CC-BY-SA-30}}
	{{Template:Coleman}}		{{Template:Coleman}}
	[[Category:DOCK 3.7]]		[[Category:DOCK 3.7]]

Frodo: Created page with "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. Once this is ..."

2014-02-13T21:35:42Z

Created page with "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. Once this is ..."

New page

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. Once this is done, make sure your PDB file looks 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. Once you're done, proceed as normal with protein receptor preparation.

{{Template:CC-BY-SA-30}}
{{Template:Coleman}}
[[Category:DOCK 3.7]]