Preparing the ligand - Revision history

Mkorcz at 00:26, 17 January 2013

2013-01-17T00:26:02Z

← Older revision		Revision as of 00:26, 17 January 2013
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	** Clean up your directory afterwards. dbgen.csh generates a lot of files that you do not need if it ran correctly.		** Clean up your directory afterwards. dbgen.csh generates a lot of files that you do not need if it ran correctly.
	*you should obtain a file <tt>somename.db.gz</tt> .		*you should obtain a file <tt>somename.db.gz</tt> .
	===
	~~WARNING this should only be done if generating conformations for a very small set of compounds!!!~~		===optional===
	To increase the number of molecules that are written out for the database generation, copy the file $DOCK_BASE/data/omega.parm into the directory that dbgen.csh is going to be run in.		To increase the number of molecules that are written out for the database generation, copy the file $DOCK_BASE/data/omega.parm into the directory that dbgen.csh is going to be run in.
	*At the end of the omega.parm file you will see a section called "Torsion Driving Parameters", here you will find three variables that can be changed.		*At the end of the omega.parm file you will see a section called "Torsion Driving Parameters", here you will find three variables that can be changed.
	SetMaxConfs(600) #set to higher numbers ie. 1000		***SetMaxConfs(600) #set to higher numbers ie. 1000
	SetRMSThreshold(0.80) #set to lower numbers ie. 0.50		***SetRMSThreshold(0.80) #set to lower numbers ie. 0.50
	SetEnergyWindow(12.5) #can be changed but this can often generate broken molecules		***SetEnergyWindow(12.5) #can be changed but this can often generate broken molecules
			*WARNING this should only be done if generating conformations for a small set of compounds!!!

	==Manual way==		==Manual way==

Mkorcz at 00:13, 17 January 2013

2013-01-17T00:13:41Z

← Older revision		Revision as of 00:13, 17 January 2013
Line 15:		Line 15:
	** Clean up your directory afterwards. dbgen.csh generates a lot of files that you do not need if it ran correctly.		** Clean up your directory afterwards. dbgen.csh generates a lot of files that you do not need if it ran correctly.
	*you should obtain a file <tt>somename.db.gz</tt> .		*you should obtain a file <tt>somename.db.gz</tt> .
			===
	WARNING this should only be done if generating conformations for a very small set of compounds!!!		WARNING this should only be done if generating conformations for a very small set of compounds!!!
	To increase the number of molecules that are written out for the database generation, copy the file $DOCK_BASE/data/omega.parm into the directory that dbgen.csh is going to be run in.		To increase the number of molecules that are written out for the database generation, copy the file $DOCK_BASE/data/omega.parm into the directory that dbgen.csh is going to be run in.

Mkorcz at 00:13, 17 January 2013

2013-01-17T00:13:12Z

← Older revision		Revision as of 00:13, 17 January 2013
Line 15:		Line 15:
	** Clean up your directory afterwards. dbgen.csh generates a lot of files that you do not need if it ran correctly.		** Clean up your directory afterwards. dbgen.csh generates a lot of files that you do not need if it ran correctly.
	*you should obtain a file <tt>somename.db.gz</tt> .		*you should obtain a file <tt>somename.db.gz</tt> .

			WARNING this should only be done if generating conformations for a very small set of compounds!!!
			To increase the number of molecules that are written out for the database generation, copy the file $DOCK_BASE/data/omega.parm into the directory that dbgen.csh is going to be run in.
			*At the end of the omega.parm file you will see a section called "Torsion Driving Parameters", here you will find three variables that can be changed.
			SetMaxConfs(600) #set to higher numbers ie. 1000
			SetRMSThreshold(0.80) #set to lower numbers ie. 0.50
			SetEnergyWindow(12.5) #can be changed but this can often generate broken molecules


	==Manual way==		==Manual way==

Therese: 9 revisions

2012-10-08T20:31:20Z

9 revisions

← Older revision

Revision as of 20:31, 8 October 2012

Tbalius: /* Automatic way, starting from SMILES */

2012-07-31T21:15:25Z

Automatic way, starting from SMILES

← Older revision		Revision as of 21:15, 31 July 2012
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	==Automatic way, starting from SMILES==		==Automatic way, starting from SMILES==

	This way will make use of John's automatic scripts for database		This way, you will make use of John's automatic scripts for database
	preparation and actually upload new molecules to a special section of		preparation and actually upload new molecules to a special section of
	[http://zinc.docking.org/ ZINC].		[http://zinc.docking.org/ ZINC].
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	*OPTIONAL: run <tt>convert.py --i=yourname.smi --o=yourname.ism</tt> . This will convert your SMILES to ''isomeric'' SMILES.		*OPTIONAL: run <tt>convert.py --i=yourname.smi --o=yourname.ism</tt> . This will convert your SMILES to ''isomeric'' SMILES.
	*run <tt>dbgen.csh yourname.smi</tt>.		*run <tt>dbgen.csh yourname.smi</tt>.
	*Note that the dbgen.csh does not work ~~well~~ for more that 1000 molecules. Brake up your molecules into chunks of 1000 and run dbgen on each chunk.		** Note that the dbgen.csh does not work for more that 1000 molecules.
			** Brake up your molecules into chunks of 1000 and run dbgen on each chunk.
			** Clean up your directory afterwards. dbgen.csh generates a lot of files that you do not need if it ran correctly.
	*you should obtain a file <tt>somename.db.gz</tt> .		*you should obtain a file <tt>somename.db.gz</tt> .

Tbalius: /* Automatic way, starting from SMILES */

2012-07-31T20:50:14Z

Automatic way, starting from SMILES

← Older revision		Revision as of 20:50, 31 July 2012
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	*OPTIONAL: run <tt>convert.py --i=yourname.smi --o=yourname.ism</tt> . This will convert your SMILES to ''isomeric'' SMILES.		*OPTIONAL: run <tt>convert.py --i=yourname.smi --o=yourname.ism</tt> . This will convert your SMILES to ''isomeric'' SMILES.
	*run <tt>dbgen.csh yourname.smi</tt>.		*run <tt>dbgen.csh yourname.smi</tt>.
			*Note that the dbgen.csh does not work well for more that 1000 molecules. Brake up your molecules into chunks of 1000 and run dbgen on each chunk.
	*you should obtain a file <tt>somename.db.gz</tt> .		*you should obtain a file <tt>somename.db.gz</tt> .

Mysinger at 02:55, 5 December 2009

2009-12-05T02:55:07Z

← Older revision		Revision as of 02:55, 5 December 2009
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	[[Category:Manual_DOCK]]		[[Category:Manual_DOCK]]
			[[Category:Tutorials]]

Mysinger: /* Running amsol */

2009-03-18T22:27:21Z

Running amsol

← Older revision		Revision as of 22:27, 18 March 2009
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	*find more information about amsol [http://comp.chem.umn.edu/amsol/ on its homepage].		*find more information about amsol [http://comp.chem.umn.edu/amsol/ on its homepage].
	*<tt>mkdir ./amsol2</tt>		*<tt>mkdir ./amsol2</tt>
	Use file2file.py to get the right formal charge to feed to AMSOL. It is also important to change the name, otherwise the original <tt>.mol2</tt> file will be overwritten!		*Use file2file.py to get the right formal charge to feed to AMSOL. It is also important to change the name, otherwise the original <tt>.mol2</tt> file will be overwritten!
	*<tt>file2file.py -g ligandname.mol2 ./amsol2/someothername.mol2</tt>		<tt>file2file.py -g ligandname.mol2 ./amsol2/someothername.mol2</tt>
	*edit <tt>./amsol2/someothername.mol2</tt> :		*edit <tt>./amsol2/someothername.mol2</tt> :
	*		*

Mysinger: /* Running amsol */

2009-03-18T22:26:19Z

Running amsol

← Older revision		Revision as of 22:26, 18 March 2009
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	*find more information about amsol [http://comp.chem.umn.edu/amsol/ on its homepage].		*find more information about amsol [http://comp.chem.umn.edu/amsol/ on its homepage].
	*<tt>mkdir ./amsol2</tt>		*<tt>mkdir ./amsol2</tt>
	*<tt>file2file.py -g ligandname.mol2 ./amsol2/someothername.mol2</tt> Uses file2file.py to get the right formal charge ~~for~~ AMSOL. It is also important to change the name, otherwise the original <tt>.mol2</tt> file will be overwritten!		Use file2file.py to get the right formal charge to feed to AMSOL. It is also important to change the name, otherwise the original <tt>.mol2</tt> file will be overwritten!
			*<tt>file2file.py -g ligandname.mol2 ./amsol2/someothername.mol2</tt>
	*edit <tt>./amsol2/someothername.mol2</tt> :		*edit <tt>./amsol2/someothername.mol2</tt> :
	*		*

Mysinger: /* Running amsol */

2009-03-18T22:23:37Z

Running amsol

New page

=Preparing a ligand=

==Automatic way, starting from SMILES==

This way will make use of John's automatic scripts for database
preparation and actually upload new molecules to a special section of
[http://zinc.docking.org/ ZINC].

*it is advisable to create a special subdirectory, since many new files will be generated.
*the file containing the [http://www.daylight.com/smiles/ SMILES] strings should contain a string followed by an identifier on each line.
*OPTIONAL: run <tt>convert.py --i=yourname.smi --o=yourname.ism</tt> . This will convert your SMILES to ''isomeric'' SMILES.
*run <tt>dbgen.csh yourname.smi</tt>.
*you should obtain a file <tt>somename.db.gz</tt> .

==Manual way==

===Isolating the ligand as <tt>.mol2</tt> file===

*extract the ligand structure from the <tt>.pdb</tt> file.
*assign hydrogens.
*assign all atom ([http://www.tripos.com/mol2/atom_types.html Sybyl/TAFF]) and bond types.
*save it as <tt>ligandname.mol2</tt> file.

===Running <tt>omega</tt> ===

*run [http://www.eyesopen.com/products/applications/omega.html OMEGA], but don't ask me how to do that yet.

===Running amsol===

*find more information about amsol [http://comp.chem.umn.edu/amsol/ on its homepage].
*<tt>mkdir ./amsol2</tt>
*<tt>file2file.py -g ligandname.mol2 ./amsol2/someothername.mol2</tt> Uses file2file.py to get the right formal charge for AMSOL. It is also important to change the name, otherwise the original <tt>.mol2</tt> file will be overwritten!
*edit <tt>./amsol2/someothername.mol2</tt> :
*
*delete all lines prior to <tt>@<TRIPOS>MOLECULE</tt>
*
*change line 2 (molecule name) to something of the format <tt>ABCD12345678</tt> (four capital letters followed by eight numbers).
*
*line 3 should be <tt>n<sub>atoms</sub> n<sub>bonds</sub> 0 0 0</tt>
*
*the <tt>@<TRIPOS>MOLECULE</tt> section must consist of exactly '''5''' lines (adjust by adding/deleting blanks).
*
*remove all sections after the <tt>@<TRIPOS>BOND</tt> section.
*
*delete the blank lines between the <tt>ATOM</tt> and <tt>BOND</tt> sections, if there are any.
*run <tt>RunAMSOL3.csh WAIT</tt>
*the output <tt>someothername.solv</tt> file will contain the following:
{| style="text-align: center; border:1px solid #aaa; margin: 1em 1em 1em 0; background: #f9f9f9; border-collapse: collapse;" cellpadding="5" cellspacing="0"
|+ '''AMSOL output'''
|-
! style="border:1px #aaa solid; padding: 0.2em;" | line #1
| style="border:1px #aaa solid; padding: 0.2em;" | molname || style="border:1px #aaa solid; padding: 0.2em;" | <math>n_{atoms}</math> || style="border:1px #aaa solid; padding: 0.2em;" | charge || style="border:1px #aaa solid; padding: 0.2em;" | pol_solv || style="border:1px #aaa solid; padding: 0.2em;" | ? || style="border:1px #aaa solid; padding: 0.2em;" | apol_solv || style="border:1px #aaa solid; padding: 0.2em;" | total_solv
|-
! style="border:1px #aaa solid; padding: 0.2em;" | other lines
| style="border:1px #aaa solid; padding: 0.2em;" | charge || style="border:1px #aaa solid; padding: 0.2em;" | pol_solv || style="border:1px #aaa solid; padding: 0.2em;" | ? || style="border:1px #aaa solid; padding: 0.2em;" | apol_solv || style="border:1px #aaa solid; padding: 0.2em;" | total_solv
|-
| style="border:1px #aaa solid; padding: 0.2em;" | ''(per_atom)''
|}

*furthermore, there will be <tt>someothername.nmol2</tt> file which contains the correct partial charges.

===Running <tt>mol2db</tt> ===

*edit <tt>someothername.nmol2</tt> so that the <tt>@<TRIPOS>MOLECULE</tt> section consists of exactly '''6''' lines.
*edit the <tt>inhier</tt> file so that the 'mol2_file', 'db_file' and 'solvation_table' entries are correct.
*run <tt>mol2db inhier</tt>
*add the preamble at the top of the file.
*<tt>gzip</tt> the resulting file so that it can be used by <tt>DOCK</tt> .

[[Category:Manual_DOCK]]