Calculate DOCK6 RMSD - Revision history

Frodo at 16:09, 14 February 2014

2014-02-14T16:09:52Z

← Older revision		Revision as of 16:09, 14 February 2014
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	[[Category:Internal]]		[[Category:Internal]]
	[[Category:Docking]]		[[Category:Docking]]
	[[Category:~~Tutorial~~]]		[[Category:Tutorials]]

Frodo at 02:58, 14 February 2014

2014-02-14T02:58:44Z

← Older revision		Revision as of 02:58, 14 February 2014
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	calc_dock6_rmsd.csh (see code below) outputs three lines:		calc_dock6_rmsd.csh (see code below) outputs three lines:

	HA_RMSDs: 4.2878 <br>		HA_RMSDs: 4.2878 <br>
	HA_RMSDh: 2.7406 <br>		HA_RMSDh: 2.7406 <br>
	HA_RMSDm: 0.9625		HA_RMSDm: 0.9625

	The most meaningful line is the one in the middle (HA_RMSDh), which outputs the RMSD using the Hungarian Algorithm (for more information: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm)		The most meaningful line is the one in the middle (HA_RMSDh), which outputs the RMSD using the Hungarian Algorithm (for more information: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm)
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	===calc_dock6_rmsd.csh===		===calc_dock6_rmsd.csh===
			<pre>
	#!/bin/csh -f		#!/bin/csh -f
	if ($#argv != 2) then		if ($#argv != 2) then
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	grep "HA_RMSD" output_scored.mol2		grep "HA_RMSD" output_scored.mol2
			</pre>

	==Acknowledgments==		==Acknowledgments==
	Thanks to Trent for pointing out this great new feature in DOCK 6.6.		Thanks to Trent for pointing out this great new feature in DOCK 6.6.


			[[Category:Internal]]
			[[Category:Docking]]
			[[Category:Tutorial]]

Oliv Eidam at 23:37, 6 May 2013

2013-05-06T23:37:23Z

← Older revision		Revision as of 23:37, 6 May 2013
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	grep "HA_RMSD" output_scored.mol2		grep "HA_RMSD" output_scored.mol2


			==Acknowledgments==
			Thanks to Trent for pointing out this great new feature in DOCK 6.6.

Oliv Eidam at 22:03, 6 May 2013

2013-05-06T22:03:17Z

← Older revision		Revision as of 22:03, 6 May 2013
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	echo "calculates rmsd between 2 molecules using hungarian algorithm implemented in DOCK 6"		echo "calculates rmsd between 2 molecules using hungarian algorithm implemented in DOCK 6"
	endif		endif

			setenv dock66_dir "/raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook"

	echo "ligand_atom_file $1" > temp.in		echo "ligand_atom_file $1" > temp.in
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	echo "score_molecules no" >> temp.in		echo "score_molecules no" >> temp.in
	echo "atom_model all" >> temp.in		echo "atom_model all" >> temp.in
	echo "vdw_defn_file ~~/raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook~~/parameters/vdw_AMBER_parm99.defn" >> temp.in		echo "vdw_defn_file $dock66_dir/parameters/vdw_AMBER_parm99.defn" >> temp.in
	echo "flex_defn_file ~~/raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook~~/parameters/flex.defn" >> temp.in		echo "flex_defn_file $dock66_dir/parameters/flex.defn" >> temp.in
	echo "flex_drive_file ~~/raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook~~/parameters/flex_drive.tbl" >> temp.in		echo "flex_drive_file $dock66_dir/parameters/flex_drive.tbl" >> temp.in
	echo "ligand_outfile_prefix output" >> temp.in		echo "ligand_outfile_prefix output" >> temp.in
	echo "write_orientations no" >> temp.in		echo "write_orientations no" >> temp.in
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	~~/raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook~~/bin/dock6 -i temp.in > dock6.log		$dock66_dir/bin/dock6 -i temp.in > dock6.log

	grep "HA_RMSD" output_scored.mol2		grep "HA_RMSD" output_scored.mol2

Oliv Eidam at 22:52, 29 April 2013

2013-04-29T22:52:22Z

← Older revision		Revision as of 22:52, 29 April 2013
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	Calculating ligand RMSDs is a tricky thing, but DOCK6 does this quite well.		Calculating ligand RMSDs is a tricky thing, but DOCK6 does this quite well.
	All you need is two ligands (with the same number of atoms and same Sybil atom types) ~~in mol2 format~~.		All you need is two ligands in mol2 format (with the same number of atoms and same Sybil atom types) and a DOCK6 binary.

	Then you run the following command:		Then you run the following command:

Oliv Eidam: Created page with "==Calculate ligand RMSDs using DOCK6== Calculating ligand RMSDs is a tricky thing, but DOCK6 does this quite well. All you need is two ligands (with the same number of atoms..."

2013-04-29T22:50:56Z

Created page with "==Calculate ligand RMSDs using DOCK6== Calculating ligand RMSDs is a tricky thing, but DOCK6 does this quite well. All you need is two ligands (with the same number of atoms..."

New page

==Calculate ligand RMSDs using DOCK6==

Calculating ligand RMSDs is a tricky thing, but DOCK6 does this quite well.
All you need is two ligands (with the same number of atoms and same Sybil atom types) in mol2 format.

Then you run the following command:

~eidamo/work/scripts/calc_dock6_rmsd.csh xtal.mol2 dock.mol2

calc_dock6_rmsd.csh (see code below) outputs three lines:

HA_RMSDs: 4.2878 <br>
HA_RMSDh: 2.7406 <br>
HA_RMSDm: 0.9625

The most meaningful line is the one in the middle (HA_RMSDh), which outputs the RMSD using the Hungarian Algorithm (for more information: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm)

===calc_dock6_rmsd.csh===

#!/bin/csh -f
if ($#argv != 2) then
echo "Usage: $0 mol.mol2 ref.mol2"
echo "calculates rmsd between 2 molecules using hungarian algorithm implemented in DOCK 6"
endif

echo "ligand_atom_file $1" > temp.in
echo "limit_max_ligands no" >> temp.in
echo "skip_molecule no" >> temp.in
echo "read_mol_solvation no" >> temp.in
echo "calculate_rmsd yes" >> temp.in
echo "use_rmsd_reference_mol yes" >> temp.in
echo "rmsd_reference_filename $2" >> temp.in
echo "use_database_filter no" >> temp.in
echo "orient_ligand no" >> temp.in
echo "use_internal_energy no" >> temp.in
echo "flexible_ligand no" >> temp.in
echo "bump_filter no" >> temp.in
echo "score_molecules no" >> temp.in
echo "atom_model all" >> temp.in
echo "vdw_defn_file /raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook/parameters/vdw_AMBER_parm99.defn" >> temp.in
echo "flex_defn_file /raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook/parameters/flex.defn" >> temp.in
echo "flex_drive_file /raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook/parameters/flex_drive.tbl" >> temp.in
echo "ligand_outfile_prefix output" >> temp.in
echo "write_orientations no" >> temp.in
echo "num_scored_conformers 1" >> temp.in
echo "rank_ligands no" >> temp.in

/raid1/people/tbalius/zzz.programs/dock6_2012-10-09.stonybrook/bin/dock6 -i temp.in > dock6.log

grep "HA_RMSD" output_scored.mol2