Working With Metal Ions - Revision history

Jma at 21:05, 6 January 2010

2010-01-06T21:05:38Z

← Older revision		Revision as of 21:05, 6 January 2010
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	*re_h2o_cu.inp: input file for cns refinement<br>		*re_h2o_cu.inp: input file for cns refinement<br>

	~~-Gaohua Liu- 2009~~<br>		<br>

Gliu at 17:28, 4 January 2010

2010-01-04T17:28:46Z

← Older revision		Revision as of 17:28, 4 January 2010
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	alias cns1 /farm/software/cns/cns_solve_1.1/intel-i686-linux_g77/bin/cns		alias cns1 /farm/software/cns/cns_solve_1.1/intel-i686-linux_g77/bin/cns

	setenv CNS_TOPPAR /farm/data/gliu/cns1/~~</pre>~~		setenv CNS_TOPPAR /farm/data/gliu/cns1/

	In addition to the topology and parameter files, the metal ion parameter file <tt>ion.top</tt> is required. An example can be found in "cns_cuttha_cis" with all required input files.		In addition to the topology and parameter files, the metal ion parameter file <tt>ion.top</tt> is required. An example can be found in "cns_cuttha_cis" with all required input files.

Gliu at 17:28, 4 January 2010

2010-01-04T17:28:09Z

← Older revision		Revision as of 17:28, 4 January 2010
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	<br> For manual CNS refinement please do the refinement as following:		<br> For manual CNS refinement please do the refinement as following:

	<br> 1.  Set environment for CNS1.1 by run: &~~lt;pre> alias cns1 /farm/software/cns/cns_solve_1.1/intel-i686-linux_g77/bin/cns</pre&gt~~;		<br> 1.  Set environment for CNS1.1 by run:

	<br>		<br>

	setenv CNS_TOPPAR /farm/data/gliu/cns1/</pre>		alias cns1 /farm/software/cns/cns_solve_1.1/intel-i686-linux_g77/bin/cns

			setenv CNS_TOPPAR /farm/data/gliu/cns1/</pre>

	In addition to the topology and parameter files, the metal ion parameter file <tt>ion.top</tt> is required. An example can be found in "~~/farm/users/gliu/projects/~~cns_cuttha_cis" with all required input files. 2.  Prepared required files as described above (final.tbl, final cns format PDB files and put in xplorPDB dir with name as sa_#.pdb) except the PDB file should include the metal ions with format according to [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/CNS CNS] library <tt>ion.top</tt>. cp sa_1.pdb as  template.pdb, input files for creating mtf file Note that alignment is important. eg:		In addition to the topology and parameter files, the metal ion parameter file <tt>ion.top</tt> is required. An example can be found in "cns_cuttha_cis" with all required input files.

			2.  Prepared required files as described above (final.tbl, final cns format PDB files and put in xplorPDB dir with name as sa_#.pdb) except the PDB file should include the metal ions with format according to [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/CNS CNS] library <tt>ion.top</tt>. cp sa_1.pdb as  template.pdb, input files for creating mtf file Note that alignment is important. eg:
	<pre>ATOM 1249 OT2 ALA 83 69.296 13.232 5.744 1.00 0.00		<pre>ATOM 1249 OT2 ALA 83 69.296 13.232 5.744 1.00 0.00
	ATOM 1250 ZN+2 ZN2 150 63.086 13.789 -10.407 1.00 0.00 zinc</pre>		ATOM 1250 ZN+2 ZN2 150 63.086 13.789 -10.407 1.00 0.00 zinc</pre>
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	6.  Edit and run re_h2o_cu.inp, the refined pdb is kept in refinedPDB, or		6.  Edit and run re_h2o_cu.inp, the refined pdb is kept in refinedPDB, or

	7.  Use ~~subcns~~ to submit cns refinement ~~by using PBS~~: eg, type "sh subcns". Before run subcns , make a folder " com" contains the following file. Type getpdb to get refined pdb files in refinedPDB after it finished.		7.  Use PBS to submit cns refinement parallal: eg, type "sh subcns". Before run subcns , make a folder " com" contains the following file. Type getpdb to get refined pdb files in refinedPDB after it finished.

	*cns.sc: PBS submission		*cns.sc: PBS submission

Gliu at 17:24, 4 January 2010

2010-01-04T17:24:19Z

← Older revision		Revision as of 17:24, 4 January 2010
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	<br> For manual CNS refinement please do the refinement as following:		<br> For manual CNS refinement please do the refinement as following:

	<br> 1.  Set environment for CNS1.1 by run ~~source /farm/users/gliu/alias.cns~~ <pre> alias cns1 /farm/software/cns/cns_solve_1.1/intel-i686-linux_g77/bin/cns		<br> 1.  Set environment for CNS1.1 by run: <pre> alias cns1 /farm/software/cns/cns_solve_1.1/intel-i686-linux_g77/bin/cns</pre>

	<br>		<br>

Gliu at 17:21, 4 January 2010

2010-01-04T17:21:37Z

← Older revision		Revision as of 17:21, 4 January 2010
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	##ION:ion residue contain only one metal ion "ME"<br>		##ION:ion residue contain only one metal ion "ME"<br>
	##PL/LP: pseudo link residues  from protein to "ION" / "ION" to protein		##PL/LP: pseudo link residues  from protein to "ION" / "ION" to protein
	##LL5" psdudo link residues		##LL5: psdudo link residues
	##CYSZ: Zinc attached cystine with cystine.SG convanlently  binds to zinc.		##CYSZ: Zinc attached cystine with cystine.SG convanlently  binds to zinc.
	##CYSS, cystine residue without "HG" atom		##CYSS: cystine residue without "HG" atom
	##CYS-, negative charged cystine residue without "HG" atom		##CYS-:  negative charged cystine residue without "HG" atom
	#Modify the protein's sequence file to have the required special residues included		#Modify the protein's sequence file to have the required special residues included
	##Using metal ion attached residues (need pay attention to the charge), eg:		##Using metal ion attached residues (need pay attention to the charge), eg:
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	LL5 LL5 LL5 LL5 LL5		LL5 LL5 LL5 LL5 LL5
	ION </pre>		ION </pre>
	#Upl/lol/aco constraints. Use reliable metal-ligand geometry parameters to derive upper/lower distance limits and angle constraints, and treated as addtional manual constraints during CYANA calculation. eg:		#Upl/lol/aco constraints. Use reliable metal-ligand geometry parameters to derive upper/lower distance limits and angle constraints, and treated as addtional manual constraints during CYANA calculation. eg:
	<pre> 78 CYSZ ZN 81 CYS- SG 2.30 5E01		<pre> 78 CYSZ ZN 81 CYS- SG 2.30 5E01
	78 CYSZ ZN 98 HIS NE2 2.40 5E01		78 CYSZ ZN 98 HIS NE2 2.40 5E01
	78 CYSZ ZN 105 CYS- SG 2.30 5E01		78 CYSZ ZN 105 CYS- SG 2.30 5E01
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	81 CYS- SG 98 HIS NE2 3.75 5E01		81 CYS- SG 98 HIS NE2 3.75 5E01
	81 CYS- SG 105 CYS- SG 3.65 5E01		81 CYS- SG 105 CYS- SG 3.65 5E01
	98 HIS NE2 105 CYS- SG 3.75 5E01</pre>		98 HIS NE2 105 CYS- SG 3.75 5E01</pre>
	#<br>		<br>

	<br>		<br>

Gliu at 17:19, 4 January 2010

2010-01-04T17:19:39Z

← Older revision		Revision as of 17:19, 4 January 2010
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	PL		PL
	LL5 LL5 LL5 LL5 LL5		LL5 LL5 LL5 LL5 LL5
	ION </pre>		ION </pre>
	#~~Metal~~-ligand geometry ~~parameters. Use reliable bond length and bond angle~~ parameters to derive upper/lower distance limits and angle constraints, and treated as addtional manual constraints during CYANA calculation.		#Upl/lol/aco constraints. Use reliable metal-ligand geometry parameters to derive upper/lower distance limits and angle constraints, and treated as addtional manual constraints during CYANA calculation. eg:
			<pre> 78 CYSZ ZN 81 CYS- SG 2.30 5E01
			78 CYSZ ZN 98 HIS NE2 2.40 5E01
			78 CYSZ ZN 105 CYS- SG 2.30 5E01
			78 CYSZ SG 81 CYS- SG 3.65 5E01
			78 CYSZ SG 98 HIS NE2 3.75 5E01
			78 CYSZ SG 105 CYS- SG 3.65 5E01
			81 CYS- SG 98 HIS NE2 3.75 5E01
			81 CYS- SG 105 CYS- SG 3.65 5E01
			98 HIS NE2 105 CYS- SG 3.75 5E01</pre>
			#<br>

	<br>		<br>

Gliu at 17:15, 4 January 2010

2010-01-04T17:15:25Z

← Older revision		Revision as of 17:15, 4 January 2010
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	##CYS-, negative charged cystine residue without "HG" atom		##CYS-, negative charged cystine residue without "HG" atom
	#Modify the protein's sequence file to have the required special residues included		#Modify the protein's sequence file to have the required special residues included
	##Using metal ion attached residues (need pay attention to the charge), eg: ~~<br>~~		##Using metal ion attached residues (need pay attention to the charge), eg:
	<pre>		<pre> VAL 76

	VAL 76
	GLN 77		GLN 77
	CYSZ 78		CYSZ 78
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	ALA 80		ALA 80
	CYS- 81		CYS- 81
	GLY 82		GLY 82 </pre>

	</pre>
	##Using psedo link, eg:		##Using psedo link, eg:
	<pre> VAL 76		<pre> VAL 76
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	PL		PL
	LL5 LL5 LL5 LL5 LL5		LL5 LL5 LL5 LL5 LL5
	ION		ION </pre>
			#Metal-ligand geometry parameters. Use reliable bond length and bond angle parameters to derive upper/lower distance limits and angle constraints, and treated as addtional manual constraints during CYANA calculation.

	</pre>
	~~<br>~~ #Metal-ligand geometry parameters. Use reliable bond length and bond angle parameters to derive upper/lower distance limits and angle constraints, and treated as addtional manual constraints during CYANA calculation.

	<br>		<br>

Gliu at 17:13, 4 January 2010

2010-01-04T17:13:04Z

← Older revision		Revision as of 17:13, 4 January 2010
Line 19:		Line 19:
	##CYS-, negative charged cystine residue without "HG" atom		##CYS-, negative charged cystine residue without "HG" atom
	#Modify the protein's sequence file to have the required special residues included		#Modify the protein's sequence file to have the required special residues included
	##Using metal ion attached residues (need pay attention to the charge), eg: <br>		##Using metal ion attached residues (need pay attention to the charge), eg: <br>
	<pre>		<pre>

Line 30:		Line 30:
	GLY 82		GLY 82

	</pre>		</pre>
	##Using psedo link, eg:		##Using psedo link, eg:
	<pre> VAL 76		<pre> VAL 76

Gliu at 17:11, 4 January 2010

2010-01-04T17:11:12Z

← Older revision		Revision as of 17:11, 4 January 2010
Line 19:		Line 19:
	##CYS-, negative charged cystine residue without "HG" atom		##CYS-, negative charged cystine residue without "HG" atom
	#Modify the protein's sequence file to have the required special residues included		#Modify the protein's sequence file to have the required special residues included
	##Using metal ion attached residues (need pay attention to the charge), eg: <br> <pre> ~~...~~		##Using metal ion attached residues (need pay attention to the charge), eg: <br>
			<pre>

	VAL 76		VAL 76
	GLN 77		GLN 77
Line 28:		Line 30:
	GLY 82		GLY 82

	~~... <br>~~ </pre>		</pre>
	##Using psedo link, eg:		##Using psedo link, eg:
	<pre>		<pre> VAL 76
	VAL 76
	GLN 77		GLN 77
	CYSS 78		CYSS 78
Line 49:		Line 50:

	</pre>		</pre>
	<br> #Metal-ligand geometry parameters. Use reliable bond length and bond angle parameters to derive upper/lower distance limits and angle constraints, and treated as addtional manual constraints during CYANA calculation.		<br> #Metal-ligand geometry parameters. Use reliable bond length and bond angle parameters to derive upper/lower distance limits and angle constraints, and treated as addtional manual constraints during CYANA calculation.

	<br>		<br>

Gliu at 17:09, 4 January 2010

2010-01-04T17:09:19Z

← Older revision		Revision as of 17:09, 4 January 2010
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	CYS- 81		CYS- 81
	GLY 82		GLY 82
	... </pre> ~~<br>~~ ##Using psedo link, eg: <pre>
			... <br> </pre>
			##Using psedo link, eg:
			<pre>
	VAL 76		VAL 76
	GLN 77		GLN 77
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	CYSS 81		CYSS 81
	GLY 82		GLY 82




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	LL5 LL5 LL5 LL5 LL5		LL5 LL5 LL5 LL5 LL5
	ION		ION
	</pre> <br> #Metal-ligand geometry parameters. Use reliable bond length and bond angle parameters to derive upper/lower distance limits and angle constraints, and treated as addtional manual constraints during CYANA calculation.


			</pre>
			<br> #Metal-ligand geometry parameters. Use reliable bond length and bond angle parameters to derive upper/lower distance limits and angle constraints, and treated as addtional manual constraints during CYANA calculation.

			<br>

	== '''Running CNS for Proteins with Metal Ions''' ==		== '''Running CNS for Proteins with Metal Ions''' ==


	The CNS refinement for proteins with metal ions can also be performed with the new WaterrefCNS script, using the appropriate metal ion nomenclature in both the pdb coordinates and distance constraints.		The CNS refinement for proteins with metal ions can also be performed with the new WaterrefCNS script, using the appropriate metal ion nomenclature in both the pdb coordinates and distance constraints.

			<br> For manual CNS refinement please do the refinement as following:

	~~For manual CNS refinement please do the refinement as following:~~		<br> 1.  Set environment for CNS1.1 by run source /farm/users/gliu/alias.cns <pre> alias cns1 /farm/software/cns/cns_solve_1.1/intel-i686-linux_g77/bin/cns


	~~1.  Set environment for CNS1.1 by run source /farm/users/gliu/alias.cns~~		<br>
	~~<pre> alias cns1 /farm/software/cns/cns_solve_1.1/intel-i686-linux_g77/bin/cns~~

			setenv CNS_TOPPAR /farm/data/gliu/cns1/</pre>

	~~setenv CNS_TOPPAR /farm/data/gliu/cns1/</pre>~~
	In addition to the topology and parameter files, the metal ion parameter file <tt>ion.top</tt> is required. An example can be found in "/farm/users/gliu/projects/cns_cuttha_cis" with all required input files. 2.  Prepared required files as described above (final.tbl, final cns format PDB files and put in xplorPDB dir with name as sa_#.pdb) except the PDB file should include the metal ions with format according to [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/CNS CNS] library <tt>ion.top</tt>. cp sa_1.pdb as  template.pdb, input files for creating mtf file Note that alignment is important. eg:		In addition to the topology and parameter files, the metal ion parameter file <tt>ion.top</tt> is required. An example can be found in "/farm/users/gliu/projects/cns_cuttha_cis" with all required input files. 2.  Prepared required files as described above (final.tbl, final cns format PDB files and put in xplorPDB dir with name as sa_#.pdb) except the PDB file should include the metal ions with format according to [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/CNS CNS] library <tt>ion.top</tt>. cp sa_1.pdb as  template.pdb, input files for creating mtf file Note that alignment is important. eg:
	<pre>ATOM 1249 OT2 ALA 83 69.296 13.232 5.744 1.00 0.00		<pre>ATOM 1249 OT2 ALA 83 69.296 13.232 5.744 1.00 0.00