ChargeCalculator:Job submission - Revision history

Crina: /* Upload molecules */

2015-05-29T17:33:15Z

Upload molecules

← Older revision		Revision as of 17:33, 29 May 2015
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	If bond information is not explicitly included in the input file, '''ACC''' will attempt to compute this information based on the molecular structure. This algorithm may assign wrong bond information when interatomic distances vary significantly from the expected norms. This behavior may only affect calculations using EEM parameter sets which distinguish between atom types based on bond information.		If bond information is not explicitly included in the input file, '''ACC''' will attempt to compute this information based on the molecular structure. This algorithm may assign wrong bond information when interatomic distances vary significantly from the expected norms. This behavior may only affect calculations using EEM parameter sets which distinguish between atom types based on bond information.

			For a given molecule, you may wish to visualize and analyze atomic charges which you obtained by other means than '''ACC'''. You can use one of the dedicated molecular structure formats that include atomic charges (mol2, pqr). Alternatively, you can use one or multiple wprop files or .*chrg files to supply '''ACC''' with several sets of precomputed charges for one or more molecules. The format of a .wprop file with atomic charges for a molecule with 7 atoms is:

			<pre>
			molecule name
			name of set of charges
			Charges
			RealAtomProperties
			7
			1 -0.303792368142346
			2 0.172805849402877
			3 0.850934507393088
			4 -0.665816273614449
			5 0.155665455717068
			6 0.0563610400635921
			7 0.205393963483477
			</pre>

			To let '''ACC''' know which .wprop or .*chrg files should be assigned with which molecule, you must name these files as '''MOLECULENAME_ref_UNIQUENAME.wprop''' or '''MOLECULENAME_ref_UNIQUENAME.wprop'''. The first part of the file name, ''MOLECULENAME'', must be the same as the name of the molecular structure file containing the molecule to which the set of charges will be assigned. The designation ''ref'' marks this set of charges as user defined. The last part of the file name, ''UNIQUENAME'' is any group of characters which will allow for a unique identification of this set of charges. Thus, if you are uploading the file 4DRP.pdb and wish to include 3 sets of charges that you previously computed using other means, simply name these files 4DRP_ref_1.wprop, 4DRP_ref_2.wprop and 4DRP_ref_3.wprop.

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Crina: /* Start computation */

2015-05-29T16:52:57Z

Start computation

← Older revision		Revision as of 16:52, 29 May 2015
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	=Start computation=		=Start computation=
	Before you launch the calculation, check out the summary of the setup. One computation may require more than one ''job''. Each ''job'' is uniquely defined by the molecule and its total charge, the set of EEM parameters, and the computation method. The number of ~~the~~ jobs thus depends on the number of molecules uploaded, along with the number of sets and methods chosen. Within a single computation, each job may use a different amount of time and memory resources, depending on the size of the molecule and the complexity of the computation method employed.		Before you launch the calculation, check out the summary of the setup. One computation may require more than one ''job''. Each ''job'' is uniquely defined by the molecule and its total charge, the set of EEM parameters, and the computation method. The number of jobs thus depends on the number of molecules uploaded, along with the number of sets and methods chosen. Within a single computation, each job may use a different amount of time and memory resources, depending on the size of the molecule and the complexity of the computation method employed.

	If you are satisfied with the computation setup, click ''Compute'' to launch the calculation. You may always check the progress of the calculation in real time, or at a later time using the same URL as for the ''Computation Setup'' page.		If you are satisfied with the computation setup, click ''Compute'' to launch the calculation. You may always check the progress of the calculation in real time, or at a later time using the same URL as for the ''Computation Setup'' page.
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	\|}		\|}

	Finally, if you don't know what something means or how it works, don't forget that there is plenty of help available directly on the '''ACC''' web pages. Hover the mouse over any keyword you do not understand to reveal a useful tool tip. Click on any of the buttons marking the interactive guides. Note that such guides are available for the entire '''Setup page''', and for any of its sections. Additional specialized guides are provided for the ''Sample'' calculations.		Finally, if you don't know what something means or how it works, don't forget that there is plenty of help available directly on the '''ACC''' web pages. Hover the mouse over any keyword you do not understand to reveal a useful tool tip. Click on any of the green buttons marking the interactive guides. Note that such guides are available for the entire '''Setup page''', and for any of its sections. Additional specialized guides are provided for the ''Sample'' calculations.
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	'''The complete list of keywords involved in the setup of ACC calculations is available in the [[ChargeCalculator:Index \| Index]].'''		'''The complete list of keywords involved in the setup of ACC calculations is available in the [[ChargeCalculator:Index \| Index]].'''
	'''Return to the [[ChargeCalculator:UserManual \| Table of contents]].'''		'''Return to the [[ChargeCalculator:UserManual \| Table of contents]].'''

Crina: /* Pick computation method */

2015-05-29T16:51:10Z

Pick computation method

← Older revision		Revision as of 16:51, 29 May 2015
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	You may change the method chosen by default, and ''add'' one or more methods of your choice using the ''Add'' button at the top of the ''Computation Methods'' section. Note that each unique method configuration added to the list will result in an additional '''ACC''' job, or set of jobs.		You may change the method chosen by default, and ''add'' one or more methods of your choice using the ''Add'' button at the top of the ''Computation Methods'' section. Note that each unique method configuration added to the list will result in an additional '''ACC''' job, or set of jobs.

	Even for molecules containing several thousands of atoms, our implementation of EEM is very time efficient, and you may use the method labeled as ''Full EEM''. For systems with tens of thousands of atoms, you will probably need to pick ''EEM Cutoff'', and a reasonable value for the ''Cutoff Radius'' parameter (we recommend a minimum of 10). A biomolecular complex with hundreds of thousands of atoms makes good use of the method ''EEM Cutoff Cover'' with a ''Cutoff Radius'' of 12 and ''single Precision''.		Even for molecules containing several thousands of atoms, our implementation of EEM is very time efficient, and you may use the method labeled as ''Full EEM''. For systems with tens of thousands of atoms, you will probably need to pick ''EEM Cutoff'', and a reasonable value for the ''Cutoff Radius'' parameter (we recommend a minimum of 10). A biomolecular complex with hundreds of thousands of atoms makes good use of the method ''EEM Cutoff Cover'' with a ''Cutoff Radius'' of 8 and ''single Precision''.

	If your system is solvated or includes a few key water molecules, you may want to run parallel calculations with and without the water molecules (tick the ''Ignore Waters'' option), to see how water can affect the charge distribution in the biomolecule. Note that '''ACC''' identifies water atoms if they are annotated by a residue name typically associated with water (HOH, WAT, H2O). Other residue names sometimes associated with water, such as SOL and TIP, are not considered here because the Protein Data Bank contains instances of such residues which are chemical components different from water. Thus, if you wish to ignore water which is annotated in your file as SOL or TIPx, you will need to remove these records before submitting to '''ACC'''.		If your system is solvated or includes a few key water molecules, you may want to run parallel calculations with and without the water molecules (tick the ''Ignore Waters'' option), to see how water can affect the charge distribution in the biomolecule. Note that '''ACC''' identifies water atoms if they are annotated by a residue name typically associated with water (HOH, WAT, H2O). Other residue names sometimes associated with water, such as SOL and TIP, are not considered here because the Protein Data Bank contains instances of such residues which are chemical components different from water. Thus, if you wish to ignore water which is annotated in your file as SOL or TIPx, you will need to remove these records before submitting to '''ACC'''.

Crina: /* Pick EEM parameters */

2015-05-29T16:49:15Z

Pick EEM parameters

← Older revision		Revision as of 16:49, 29 May 2015
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	\|}		\|}

	You may also ''add'' your own set of EEM parameters if you are unhappy with the built-in sets available. Click the ''Add'' button at the top of the ''EEM Parameters'' section to open a separate window where you can fill in the values of the parameters into a predefined XML template suitable for '''ACC'''. Make sure to keep the established XML syntax and give your set by a unique name, then click the ''Add'' button. '''ACC''' will verify the syntax and let you know if you need to change anything. Your new set will be available in the table, along with the built-in sets.		You may also ''add'' your own set of EEM parameters if you are unhappy with the built-in sets available. Click the ''Add'' button at the top of the ''EEM Parameters'' section to open a separate window where you can fill in the values of the parameters into a predefined XML template suitable for '''ACC'''. Make sure to keep the established XML syntax and give your set a unique name, then click the ''Add'' button. '''ACC''' will verify the syntax and let you know if you need to change anything. Your new set will be available in the table, along with the built-in sets.

	You can use the ''add'' function in order to generate modified versions of built-in sets. Click on the built-in set of interest, then ''View XML'' on the panel to the right. Copy/paste the content into the ''Add'' window and make your modifications. For example, if you copy the parameters for H into the same set, and modify the ''Element name'' tag to say P, you have added EEM parameters for phosphorus which are identical to the EEM parameters used for hydrogen. Save this EEM parameter set under a unique name, and it will be available in the table.		You can use the ''add'' function in order to generate modified versions of built-in sets. Click on the built-in set of interest, then ''View XML'' on the panel to the right. Copy/paste the content into the ''Add'' window and make your modifications. For example, if you copy the parameters for H into the same set, and modify the ''Element name'' tag to say P, you have added EEM parameters for phosphorus which are identical to the EEM parameters used for hydrogen. Save this EEM parameter set under a unique name, and it will be available in the table.

Lukas at 10:06, 28 December 2014

2014-12-28T10:06:04Z

Crina: /* Pick EEM parameters */

2014-12-24T19:29:06Z

Pick EEM parameters

← Older revision		Revision as of 19:29, 24 December 2014
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	In the table with EEM sets, check the column ''Atoms'' to see which atom types are covered by each set. '''ACC''' will let you know if a given set does not contain parameters for some atom types present in the molecule(s) you uploaded. Look for the orange highlight which marks <span style="color:#DAA520">missing parameters</span> in the column ''Missing atoms''. If parameters are not available for a certain ''atom type'', these atoms will be skipped during the EEM calculation. Note that if built-in EEM sets with all necessary parameters are available, the rest of the sets are hidden by default. To reveal them, untick the option ''Show only sets with all required parameters'' at the top of the table with sets.		In the table with EEM sets, check the column ''Atoms'' to see which atom types are covered by each set. '''ACC''' will let you know if a given set does not contain parameters for some atom types present in the molecule(s) you uploaded. Look for the orange highlight which marks <span style="color:#DAA520">missing parameters</span> in the column ''Missing atoms''. If parameters are not available for a certain ''atom type'', these atoms will be skipped during the EEM calculation. Note that if built-in EEM sets with all necessary parameters are available, the rest of the sets are hidden by default. To reveal them, untick the option ''Show only sets with all required parameters'' at the top of the table with sets.

	Select one or more EEM parameter sets for your computation. ~~Note that each~~ EEM parameter set will be associated with a different '''ACC''' job or set of jobs.		Select one or more EEM parameter sets for your computation. Pick sets which contain EEM parameters for all or most atoms in your input molecule(s), and which have lower values of the ''priority'' descriptor. Each EEM parameter set will be associated with a different '''ACC''' job or set of jobs.

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Crina: /* Upload molecules */

2014-12-24T06:38:01Z

Upload molecules

← Older revision		Revision as of 06:38, 24 December 2014
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	'''ACC''' is able to read the molecular structure and charge information from the most common file formats. Nonetheless, because it was designed to handle molecules of all kinds and size, '''ACC''' generally requires that the input files follow the formal guidelines established for each format.		'''ACC''' is able to read the molecular structure and charge information from the most common file formats. Nonetheless, because it was designed to handle molecules of all kinds and size, '''ACC''' generally requires that the input files follow the formal guidelines established for each format.

	'''Checklist for uploading molecules'''		{\| class="wikitable"
			\|-
			\|'''Checklist for uploading molecules'''
			\|-
			\|
	*File format: PDB, PDBx/mmCIF, PQR, MOL, MOL2, SDF, or .zip with multiple files of a suitable format; 50MB limit for each upload		*File format: PDB, PDBx/mmCIF, PQR, MOL, MOL2, SDF, or .zip with multiple files of a suitable format; 50MB limit for each upload
	*All H should be present, according to the appropriate protonation states. The computation can run even when H are missing, but the absolute values of the atomic charges will not be chemically relevant.		*All H should be present, according to the appropriate protonation states. The computation can run even when H are missing, but the absolute values of the atomic charges will not be chemically relevant.
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	*If a file contains multiple molecules annotated as such (typically NMR models), only the first one will be loaded. If you want to load more NMR models (e.g., to later compare the results), you need to upload them in separate files.		*If a file contains multiple molecules annotated as such (typically NMR models), only the first one will be loaded. If you want to load more NMR models (e.g., to later compare the results), you need to upload them in separate files.
	*If a molecule contains more ''chains'', the chain IDs should be present at their appropriate location.		*If a molecule contains more ''chains'', the chain IDs should be present at their appropriate location.
			\|}

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Crina: /* Upload molecules */

2014-12-20T00:37:25Z

Upload molecules

← Older revision		Revision as of 00:37, 20 December 2014
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	*All H should be present, according to the appropriate protonation states. The computation can run even when H are missing, but the absolute values of the atomic charges will not be chemically relevant.		*All H should be present, according to the appropriate protonation states. The computation can run even when H are missing, but the absolute values of the atomic charges will not be chemically relevant.
	*No limitation regarding the size, number or nature of the chemical entities in each file: proteins, nucleic acids, ligands, water... - everything will be loaded and identified as a single ''molecule''		*No limitation regarding the size, number or nature of the chemical entities in each file: proteins, nucleic acids, ligands, water... - everything will be loaded and identified as a single ''molecule''
	*If a file contains multiple molecules annotated as such (typically NMR models), only the first one will be loaded.		*If a file contains multiple molecules annotated as such (typically NMR models), only the first one will be loaded. If you want to load more NMR models (e.g., to later compare the results), you need to upload them in separate files.
	*If a molecule contains more ''chains'', the chain IDs should be present at their appropriate location.		*If a molecule contains more ''chains'', the chain IDs should be present at their appropriate location.

Crina: /* Pick computation method */

2014-12-19T14:47:41Z

Pick computation method

← Older revision		Revision as of 14:47, 19 December 2014
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	You may change the method chosen by default, and ''add'' one or more methods of your choice using the ''Add'' button at the top of the ''Computation Methods'' section. Note that each unique method configuration added to the list will result in an additional '''ACC''' job, or set of jobs.		You may change the method chosen by default, and ''add'' one or more methods of your choice using the ''Add'' button at the top of the ''Computation Methods'' section. Note that each unique method configuration added to the list will result in an additional '''ACC''' job, or set of jobs.

	Even for molecules containing several thousands of atoms, our implementation of EEM is very time efficient, and you may use the method labeled as ''EEM''. For systems with tens of thousands of atoms, you will probably need to pick ''EEM Cutoff'', and a reasonable value for the ''Cutoff Radius'' parameter (we recommend a minimum of 10). A biomolecular complex with hundreds of thousands of atoms makes good use of the method ''EEM Cutoff Cover'' with a ''Cutoff Radius'' of 12 and ''single Precision''.		Even for molecules containing several thousands of atoms, our implementation of EEM is very time efficient, and you may use the method labeled as ''Full EEM''. For systems with tens of thousands of atoms, you will probably need to pick ''EEM Cutoff'', and a reasonable value for the ''Cutoff Radius'' parameter (we recommend a minimum of 10). A biomolecular complex with hundreds of thousands of atoms makes good use of the method ''EEM Cutoff Cover'' with a ''Cutoff Radius'' of 12 and ''single Precision''.

	If your system is solvated or includes a few key water molecules, you may want to run parallel calculations with and without the water molecules (tick the ''Ignore Waters'' option), to see how water can affect the charge distribution in the biomolecule. Note that '''ACC''' identifies water atoms if they are annotated by a residue name typically associated with water (HOH, WAT, H2O). Other residue names sometimes associated with water, such as SOL and TIP, are not considered here because the Protein Data Bank contains instances of such residues which are chemical components different from water. Thus, if you wish to ignore water which is annotated in your file as SOL or TIPx, you will need to remove these records before submitting to '''ACC'''.		If your system is solvated or includes a few key water molecules, you may want to run parallel calculations with and without the water molecules (tick the ''Ignore Waters'' option), to see how water can affect the charge distribution in the biomolecule. Note that '''ACC''' identifies water atoms if they are annotated by a residue name typically associated with water (HOH, WAT, H2O). Other residue names sometimes associated with water, such as SOL and TIP, are not considered here because the Protein Data Bank contains instances of such residues which are chemical components different from water. Thus, if you wish to ignore water which is annotated in your file as SOL or TIPx, you will need to remove these records before submitting to '''ACC'''.

Crina: /* Pick computation method */

2014-12-19T14:46:50Z

Pick computation method

← Older revision		Revision as of 14:46, 19 December 2014
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	Even for molecules containing several thousands of atoms, our implementation of EEM is very time efficient, and you may use the method labeled as ''EEM''. For systems with tens of thousands of atoms, you will probably need to pick ''EEM Cutoff'', and a reasonable value for the ''Cutoff Radius'' parameter (we recommend a minimum of 10). A biomolecular complex with hundreds of thousands of atoms makes good use of the method ''EEM Cutoff Cover'' with a ''Cutoff Radius'' of 12 and ''single Precision''.		Even for molecules containing several thousands of atoms, our implementation of EEM is very time efficient, and you may use the method labeled as ''EEM''. For systems with tens of thousands of atoms, you will probably need to pick ''EEM Cutoff'', and a reasonable value for the ''Cutoff Radius'' parameter (we recommend a minimum of 10). A biomolecular complex with hundreds of thousands of atoms makes good use of the method ''EEM Cutoff Cover'' with a ''Cutoff Radius'' of 12 and ''single Precision''.

	If your system is solvated or includes a few key water molecules, you may want to run parallel calculations with and without the water molecules (tick the ''Ignore Waters'' option), to see how water can affect the charge distribution in the biomolecule.		If your system is solvated or includes a few key water molecules, you may want to run parallel calculations with and without the water molecules (tick the ''Ignore Waters'' option), to see how water can affect the charge distribution in the biomolecule. Note that '''ACC''' identifies water atoms if they are annotated by a residue name typically associated with water (HOH, WAT, H2O). Other residue names sometimes associated with water, such as SOL and TIP, are not considered here because the Protein Data Bank contains instances of such residues which are chemical components different from water. Thus, if you wish to ignore water which is annotated in your file as SOL or TIPx, you will need to remove these records before submitting to '''ACC'''.

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	=Start computation=		=Start computation=

← Older revision		Revision as of 10:06, 28 December 2014
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	The '''ACC submission page''' contains a brief description of ACC, and is further organized into several tabs. Since this is your first contact with ACC, the support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples of ACC use cases.		The '''ACC submission page''' contains a brief description of ACC, and is further organized into several tabs. Since this is your first contact with ACC, the support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples of ACC use cases.

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	\|<!--Col1-->[[File:ACC FirstTimeUserGuide 20.jpg\| 650px]]		\|<!--Col1-->[[File:ACC FirstTimeUserGuide 20.jpg\| 650px]]
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	\|<!--Col1-->[[File:ACC FirstTimeUserGuide 03.jpg\| 650px]]		\|<!--Col1-->[[File:ACC FirstTimeUserGuide 03.jpg\| 650px]]
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	Once you have uploaded your molecule(s), ACC parses the molecular structure and redirects you to the '''ACC Setup page'''. Note that at this point a ''unique URL'' has been generated on the ACC server, and assigned to your computation. You may use this URL during calculation setup, execution or completion to access all the data associated with your '''ACC''' computation.		Once you have uploaded your molecule(s), ACC parses the molecular structure and redirects you to the '''ACC Setup page'''. Note that at this point a ''unique URL'' has been generated on the ACC server, and assigned to your computation. You may use this URL during calculation setup, execution or completion to access all the data associated with your '''ACC''' computation.

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	\|<!--Col1-->[[File:ACC FirstTimeUserGuide 05.jpg\| 650px]]		\|<!--Col1-->[[File:ACC FirstTimeUserGuide 05.jpg\| 650px]]
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	Select one or more EEM parameter sets for your computation. Pick sets which contain EEM parameters for all or most atoms in your input molecule(s), and which have lower values of the ''priority'' descriptor. Each EEM parameter set will be associated with a different '''ACC''' job or set of jobs.		Select one or more EEM parameter sets for your computation. Pick sets which contain EEM parameters for all or most atoms in your input molecule(s), and which have lower values of the ''priority'' descriptor. Each EEM parameter set will be associated with a different '''ACC''' job or set of jobs.

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	\|<!--Col1-->[[File:ACC FirstTimeUserGuide 08.jpg\| 650px]]		\|<!--Col1-->[[File:ACC FirstTimeUserGuide 08.jpg\| 650px]]
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	If you are satisfied with the computation setup, click ''Compute'' to launch the calculation. You may always check the progress of the calculation in real time, or at a later time using the same URL as for the ''Computation Setup'' page.		If you are satisfied with the computation setup, click ''Compute'' to launch the calculation. You may always check the progress of the calculation in real time, or at a later time using the same URL as for the ''Computation Setup'' page.

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	\|<!--Col1-->[[File:ACC FirstTimeUserGuide 10.jpg\| 650px]]		\|<!--Col1-->[[File:ACC FirstTimeUserGuide 10.jpg\| 650px]]