Analysing the results - Revision history

Therese: 18 revisions

2012-10-08T18:10:26Z

18 revisions

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Revision as of 18:10, 8 October 2012

Mysinger: /* Atomic contributions to the desolvation */

2011-05-28T03:47:18Z

Atomic contributions to the desolvation

← Older revision		Revision as of 03:47, 28 May 2011
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	Or to generate this data yourself		Or to generate this data yourself
	*start <tt>scoreopt_so</tt> and choose option '4' in the first menu.		*start <tt>scoreopt_so</tt> and choose option '4' in the first menu.
	*enter the name of the grid for partial desolvation, presumably <tt>grids/solvmap</tt> .		*enter the name of the grid for partial desolvation, presumably <tt>grids/solvmap</tt> or <tt>grids/solvmap_sev</tt>.
	*enter the name of the ligand file, i.e., <tt>ligand.eel1</tt> .		*enter the name of the ligand file, i.e., <tt>ligand.eel1</tt> .
	*enter the name of the output file, e.g. <tt>ligand.solv</tt> .		*enter the name of the output file, e.g. <tt>ligand.solv</tt> .

	==Other small useful things==		==Other small useful things==

Mysinger: /* Atomic contributions to the coulombic energy */

2011-05-28T03:46:45Z

Atomic contributions to the coulombic energy

← Older revision		Revision as of 03:46, 28 May 2011
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	*enter the name of the DelPhi potential file, presumably <tt>grids/rec+sph.phi</tt>.		*enter the name of the DelPhi potential file, presumably <tt>grids/rec+sph.phi</tt>.
	*enter the name of the ligand file, i.e., <tt>ligand.eel1</tt> or <tt>top500.eel1</tt>.		*enter the name of the ligand file, i.e., <tt>ligand.eel1</tt> or <tt>top500.eel1</tt>.
	*enter the name of the output file, e.g. <tt>ligand.~~elec~~</tt> .		*enter the name of the output file, e.g. <tt>ligand.delphi</tt> .


	===Atomic contributions to the van der Waals energy===		===Atomic contributions to the van der Waals energy===

Mysinger: Update to the modern way to scoreopt

2011-05-28T03:46:00Z

Update to the modern way to scoreopt

← Older revision		Revision as of 03:46, 28 May 2011
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	=====For the xtal-lig.mol2 in its crystallographic pose=====		=====For the xtal-lig.mol2 in its crystallographic pose=====

	~~Convert~~ an input <tt>[http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0 .mol2]</tt> file into an <tt>.eel1</tt> file		New way that outputs your.eel1 starting from your.pdb directly
			*run '<tt>$mud/to_eel1.csh your.pdb</tt>'.

			If that fails, use the old way to convert an input <tt>[http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0 .mol2]</tt> file into an <tt>.eel1</tt> file
	*run <tt>amsol</tt> as described [[Preparing_the_ligand#Running amsol\|here]] to calculate atomic solvation energies.		*run <tt>amsol</tt> as described [[Preparing_the_ligand#Running amsol\|here]] to calculate atomic solvation energies.
	*run '<tt>file2file.py -s path/to/amsol.solv path/to/amsol.nmol2 ligand.eel1</tt>'.		*run '<tt>file2file.py -s path/to/amsol.solv path/to/amsol.nmol2 ligand.eel1</tt>'.
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	*or to create an <tt>.eel1</tt> file for a different subset of the molecules, first create the list of molecule names plus their energies (on one line) and then feed it to '<tt>getxpdb.pl name_energy.list < FF.test.eel1 > subset_name.eel1</tt>'.		*or to create an <tt>.eel1</tt> file for a different subset of the molecules, first create the list of molecule names plus their energies (on one line) and then feed it to '<tt>getxpdb.pl name_energy.list < FF.test.eel1 > subset_name.eel1</tt>'.

	===~~Individual~~ contributions to the coulombic energy===		===Overall molecular score compiled from all scoreopt_so options===

			For default grids
			*run <tt>'$mud/doscoreopt.csh your.eel1 ../path/to/grids'</tt>
			Or for custom grids, used below to run SEV-based desolvation grids
			*run <tt>'$mud/doscoreopt.csh your.eel1 ../path/to/grids rec+sph.phi chem solvmap_sev'</tt>
			The summary for the whole molecule is output to your.eel1.scores in combine.scores format

			===Atomic contributions to the coulombic energy===

			In your.eel1.delphi from the wrapper
			*in every ATOM line, columns 9, 10 and 11 are the partial charge, the electrostatic field and the energy in kT (i.e., 9 × 10) of the atom, respectively.
			*the DelPhi electrostatic score is the sum over the entries in column 11 times 0.5924 (conversion from kT to kcal/mol) and can be compared to the elect column in OUTDOCK.
			Or to generate this data yourself
	*start <tt>scoreopt_so</tt> and choose option '2' in the first menu.		*start <tt>scoreopt_so</tt> and choose option '2' in the first menu.
	*enter the name of the DelPhi potential file, presumably <tt>grids/rec+sph.phi</tt>.		*enter the name of the DelPhi potential file, presumably <tt>grids/rec+sph.phi</tt>.
	*enter the name of the ligand file, i.e., <tt>ligand.eel1</tt> or <tt>top500.eel1</tt>.		*enter the name of the ligand file, i.e., <tt>ligand.eel1</tt> or <tt>top500.eel1</tt>.
	*enter the name of the output file, e.g. <tt>ligand.elec</tt> .		*enter the name of the output file, e.g. <tt>ligand.elec</tt> .
	*in every ATOM line, columns 9, 10 and 11 are the partial charge, the electrostatic field and the energy in kT (i.e., 9 × 10) of the atom, respectively.
	*the DelPhi electrostatic score is the sum over the entries in column 11 times 0.5924 (conversion from kT to kcal/mol) and can be compared to the elect column in OUTDOCK.

	===~~Individual~~ contributions to the van der Waals energy===
			===Atomic contributions to the van der Waals energy===

			In your.eel1.vdw from the wrapper
			*be adequately [http://www.merriam-webster.com/dictionary/scared scared].
			*the van der Waals interaction energy is calculated as <math>{vdW}_{(r)}=\frac{A}{r^{12}}-\frac{B}{r^6}=a-b</math>. In every ATOM line, columns 9, 10 and 11 are <math>a</math>, <math>b</math> and <math>a-b</math>, respectively.
			* DO NOT use the interaction energy, as we only use the vdw component now. Instead, use the vdwsum to compare with the vdW column in OUTDOCK.
			Or to generate this data yourself
	*start <tt>scoreopt_so</tt> and choose option '3' in the first menu.		*start <tt>scoreopt_so</tt> and choose option '3' in the first menu.
	*enter the prefix name of grids for ff scoring as a full path, i.e., <tt>grids/chem</tt> .		*enter the prefix name of grids for ff scoring as a full path, i.e., <tt>grids/chem</tt> .
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	*enter the name of the ligand file, i.e., <tt>ligand.eel1</tt> .		*enter the name of the ligand file, i.e., <tt>ligand.eel1</tt> .
	*enter the name of the output file, e.g. <tt>ligand.vdw</tt> .		*enter the name of the output file, e.g. <tt>ligand.vdw</tt> .
	*be adequately [http://www.merriam-webster.com/dictionary/scared scared].
	*the van der Waals interaction energy is calculated as <math>{vdW}_{(r)}=\frac{A}{r^{12}}-\frac{B}{r^6}=a-b</math>. In every ATOM line, columns 9, 10 and 11 are <math>a</math>, <math>b</math> and <math>a-b</math>, respectively.
	* DO NOT use the interaction energy, as we only use the vdw component now. Instead, use the vdwsum to compare with the vdW column in OUTDOCK.

	===~~Individual~~ contributions to the desolvation===
			===Atomic contributions to the desolvation===

			In your.eel1.solv from the wrapper
			*in every ATOM line, columns 9, 10, and 11 are the total atomic solvation energy (polar + apolar), percentage desolvation, and atomic desolvation energy (i.e. - 9 × 10) of the atom, respectively.
			*the total desolvation is the sum over the entries in column 11 and can be compared to the sum of the polsol and apolsol columns in OUTDOCK.
			Or to generate this data yourself
	*start <tt>scoreopt_so</tt> and choose option '4' in the first menu.		*start <tt>scoreopt_so</tt> and choose option '4' in the first menu.
	*enter the name of the grid for partial desolvation, presumably <tt>grids/solvmap</tt> .		*enter the name of the grid for partial desolvation, presumably <tt>grids/solvmap</tt> .
	*enter the name of the ligand file, i.e., <tt>ligand.eel1</tt> .		*enter the name of the ligand file, i.e., <tt>ligand.eel1</tt> .
	*enter the name of the output file, e.g. <tt>ligand.solv</tt> .		*enter the name of the output file, e.g. <tt>ligand.solv</tt> .
	*in every ATOM line, columns 9, 10, and 11 are the total atomic solvation energy (polar + apolar), percentage desolvation, and atomic desolvation energy (i.e. - 9 × 10) of the atom, respectively.
	*the total desolvation is the sum over the entries in column 11 and can be compared to the sum of the polsol and apolsol columns in OUTDOCK.

	==Other small useful things==		==Other small useful things==

Mysinger at 02:54, 5 December 2009

2009-12-05T02:54:53Z

← Older revision		Revision as of 02:54, 5 December 2009
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	[[Category:Manual_DOCK]]		[[Category:Manual_DOCK]]
			[[Category:Tutorials]]

Mysinger: /* Getting individual atom contributions with scoreopt_so */

2009-12-05T02:53:11Z

Getting individual atom contributions with scoreopt_so

← Older revision		Revision as of 02:53, 5 December 2009
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	==Getting individual atom contributions with scoreopt_so==		==Getting individual atom contributions with scoreopt_so==

	===First you need ~~and~~ <tt>.eel1</tt> file to be scored===		===First you need an <tt>.eel1</tt> file to be scored===

	=====For the xtal-lig.mol2 in its crystallographic pose=====		=====For the xtal-lig.mol2 in its crystallographic pose=====

Mysinger: /* Some analyses that can be performed */

2009-12-05T02:52:29Z

Some analyses that can be performed

← Older revision		Revision as of 02:52, 5 December 2009
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	=Some analyses that can be performed=		=Some analyses that can be performed=

			See [[MUD - Michael's Utilities for Docking]] for a lot of tools to help with analyzing DOCK runs.

	==Combining the results of all subdirectories==		==Combining the results of all subdirectories==

Mysinger: /* Getting individual atom contributions with scoreopt_so */

2009-12-05T02:50:23Z

Getting individual atom contributions with scoreopt_so

← Older revision		Revision as of 02:50, 5 December 2009
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	===First you need and <tt>.eel1</tt> file to be scored===		===First you need and <tt>.eel1</tt> file to be scored===

	====For the xtal-lig.mol2 in its crystallographic pose====		=====For the xtal-lig.mol2 in its crystallographic pose=====

	Convert an input <tt>[http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0 .mol2]</tt> file into an <tt>.eel1</tt> file		Convert an input <tt>[http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0 .mol2]</tt> file into an <tt>.eel1</tt> file
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	*run '<tt>file2file.py -s path/to/amsol.solv path/to/amsol.nmol2 ligand.eel1</tt>'.		*run '<tt>file2file.py -s path/to/amsol.solv path/to/amsol.nmol2 ligand.eel1</tt>'.

	====For molecules that have already been docked====		=====For molecules that have already been docked=====

	*run '<tt>$mud/topdock.py -e -o top500.eel1' to generate an .eel1 containing the top 500 docked molecules.		*run '<tt>$mud/topdock.py -e -o top500.eel1' to generate an .eel1 containing the top 500 docked molecules.

Mysinger at 02:50, 5 December 2009

2009-12-05T02:50:01Z

← Older revision		Revision as of 02:50, 5 December 2009
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	===First you need and <tt>.eel1</tt> file to be scored===		===First you need and <tt>.eel1</tt> file to be scored===

	=For the xtal-lig.mol2 in its crystallographic pose=		====For the xtal-lig.mol2 in its crystallographic pose====

	Convert an input <tt>[http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0 .mol2]</tt> file into an <tt>.eel1</tt> file		Convert an input <tt>[http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0 .mol2]</tt> file into an <tt>.eel1</tt> file
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	*run '<tt>file2file.py -s path/to/amsol.solv path/to/amsol.nmol2 ligand.eel1</tt>'.		*run '<tt>file2file.py -s path/to/amsol.solv path/to/amsol.nmol2 ligand.eel1</tt>'.

	=For molecules that have already been docked=		====For molecules that have already been docked====

	*run '<tt>$mud/topdock.py -e -o top500.eel1' to generate an .eel1 containing the top 500 docked molecules.		*run '<tt>$mud/topdock.py -e -o top500.eel1' to generate an .eel1 containing the top 500 docked molecules.

Mysinger: /* Getting individual atom contributions with scoreopt_so */

2009-12-05T02:49:07Z

Getting individual atom contributions with scoreopt_so

← Older revision		Revision as of 02:49, 5 December 2009
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	==Getting individual atom contributions with scoreopt_so==		==Getting individual atom contributions with scoreopt_so==

	===~~Converting a~~ <tt>[http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0 .mol2]</tt> file into an <tt>.eel1</tt> file~~===~~		===First you need and <tt>.eel1</tt> file to be scored===

			=For the xtal-lig.mol2 in its crystallographic pose=

			Convert an input <tt>[http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0 .mol2]</tt> file into an <tt>.eel1</tt> file
	*run <tt>amsol</tt> as described [[Preparing_the_ligand#Running amsol\|here]] to calculate atomic solvation energies.		*run <tt>amsol</tt> as described [[Preparing_the_ligand#Running amsol\|here]] to calculate atomic solvation energies.
	*run <tt>file2file.py -s path/to/amsol.solv path/to/amsol.nmol2 ligand.eel1</tt>.		*run '<tt>file2file.py -s path/to/amsol.solv path/to/amsol.nmol2 ligand.eel1</tt>'.

			=For molecules that have already been docked=

			*run '<tt>$mud/topdock.py -e -o top500.eel1' to generate an .eel1 containing the top 500 docked molecules.
			*or unzip the dock output '<tt>gunzip -c test.eel1.gz > test.eel1</tt>'
			*or to create an <tt>.eel1</tt> file for a different subset of the molecules, first create the list of molecule names plus their energies (on one line) and then feed it to '<tt>getxpdb.pl name_energy.list < FF.test.eel1 > subset_name.eel1</tt>'.

	===Individual contributions to the coulombic energy===		===Individual contributions to the coulombic energy===
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	*start <tt>scoreopt_so</tt> and choose option '2' in the first menu.		*start <tt>scoreopt_so</tt> and choose option '2' in the first menu.
	*enter the name of the DelPhi potential file, presumably <tt>grids/rec+sph.phi</tt>.		*enter the name of the DelPhi potential file, presumably <tt>grids/rec+sph.phi</tt>.
	*enter the name of the ligand file, i.e., <tt>ligand.eel1</tt> .		*enter the name of the ligand file, i.e., <tt>ligand.eel1</tt> or <tt>top500.eel1</tt>.
	*enter the name of the output file, e.g. <tt>ligand.elec</tt> .		*enter the name of the output file, e.g. <tt>ligand.elec</tt> .
	*in every ATOM line, columns 9, 10 and 11 are the partial charge, the electrostatic field and the energy in kT (i.e., 9 × 10) of the atom, respectively.		*in every ATOM line, columns 9, 10 and 11 are the partial charge, the electrostatic field and the energy in kT (i.e., 9 × 10) of the atom, respectively.