ChargeCalculator:Technical details - Revision history

Crina: /* Parsing */

2015-05-29T17:19:02Z

Parsing

← Older revision		Revision as of 17:19, 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.

			'''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: /* Requirements */

2014-12-20T20:39:23Z

Requirements

← Older revision		Revision as of 20:39, 20 December 2014
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	Check if your browser is [http://get.webgl.org WebGL] and [http://www.enable-javascript.com/ Javascript] compliant.		Check if your browser is [http://get.webgl.org WebGL] and [http://www.enable-javascript.com/ Javascript] compliant.

			If you are using OS X, you might encounter problems when opening the downloaded .zip file with results. This is a known issue, and you can read about it more [http://osxdaily.com/2013/02/13/open-zip-cpgz-file/ here].

	If you prefer to run '''ACC''' on your own machine, possibly as part of much larger and more complex computational projects, a command line version of '''ACC''' is available. Its EEM, statistical and file conversion capabilities are the same as those of the '''ACC''' web server. Please read about how to use '''ACC''' in command line [[ChargeCalculator:CMD_Version \| here]].		If you prefer to run '''ACC''' on your own machine, possibly as part of much larger and more complex computational projects, a command line version of '''ACC''' is available. Its EEM, statistical and file conversion capabilities are the same as those of the '''ACC''' web server. Please read about how to use '''ACC''' in command line [[ChargeCalculator:CMD_Version \| here]].

Crina: /* Structure */

2014-12-19T12:10:31Z

Structure

← Older revision		Revision as of 12:10, 19 December 2014
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	In order to produce chemically relevant atomic charges using EEM, it is necessary that the structure of the molecule be complete. No crucial parts should be missing. If parts of the structure are missing, appropriate cappings should be included. All protons should be present according to the relevant protonation state. Since '''ACC''' does not currently include functionality for editing the molecular structure, you must address these issues prior to uploading the molecule into '''ACC'''.		In order to produce chemically relevant atomic charges using EEM, it is necessary that the structure of the molecule be complete. No crucial parts should be missing. If parts of the structure are missing, appropriate cappings should be included. All protons should be present according to the relevant protonation state. Since '''ACC''' does not currently include functionality for editing the molecular structure, you must address these issues prior to uploading the molecule into '''ACC'''.

	'''ACC''' ~~does check valences, and~~ produces a <span style="color:#DAA520">''missing H'' warning</span> if ~~they~~ are ~~not satisfied~~. Despite the warning though, '''ACC''' allows to proceed with the charge calculation step, as it might not always be possible to obtain a perfect structure (e.g., when working with low resolution structures of extremely large complexes). The results from such calculations may not have chemical meaning in their absolute values, but they can be very useful when comparing sets of charges (open vs closed conformation, free vs bound state, etc.).		'''ACC''' produces a <span style="color:#DAA520">''missing H'' warning</span> if no protons are detected in the input file. Despite the warning though, '''ACC''' allows to proceed with the charge calculation step, as it might not always be possible to obtain a perfect structure (e.g., when working with low resolution structures of extremely large complexes). The results from such calculations may not have chemical meaning in their absolute values, but they can be very useful when comparing sets of charges (open vs closed conformation, free vs bound state, etc.).

	===Total charge===		===Total charge===

Crina: /* Polarization and charge transfer */

2014-12-08T15:19:19Z

Polarization and charge transfer

← Older revision		Revision as of 15:19, 8 December 2014
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	===Polarization and charge transfer===		===Polarization and charge transfer===
	EEM, as implemented in '''ACC''', works at the atomic level, and does not see the electronic ~~structire~~. Nonetheless, due to the principle of electronegativity equalization, EEM allows electron density to spread across the molecule in a manner which depends on the nature of the atoms and the chemical environment created by the surrounding atoms. The degree to which this happens also depends on the ''charge definition'' and fitting algorithms used during the development of the EEM parameters (see also the [[ChargeCalculator:Theoretical_background \| Theoretical background ]]).		EEM, as implemented in '''ACC''', works at the atomic level, and does not see the electronic structure. Nonetheless, due to the principle of electronegativity equalization, EEM allows electron density to spread across the molecule in a manner which depends on the nature of the atoms and the chemical environment created by the surrounding atoms. The degree to which this happens also depends on the ''charge definition'' and fitting algorithms used during the development of the EEM parameters (see also the [[ChargeCalculator:Theoretical_background \| Theoretical background ]]).

	This behavior means that atomic charges in a residue depend on the conformation of the residue, as well as the conformation of nearby residues. Moreover, the total charge on each residue may differ from the expected formal charge (-1, 0, +1) due to charge transfer to the surrounding residues, ligands, ions, water, etc. While this behavior is realistic, it may not be desired for some applications.		This behavior means that atomic charges in a residue depend on the conformation of the residue, as well as the conformation of nearby residues. Moreover, the total charge on each residue may differ from the expected formal charge (-1, 0, +1) due to charge transfer to the surrounding residues, ligands, ions, water, etc. While this behavior is realistic, it may not be desired for some applications.

Crina: /* Requirements */

2014-12-05T20:48:12Z

Requirements

← Older revision		Revision as of 20:48, 5 December 2014
Line 6:		Line 6:

	Check if your browser is [http://get.webgl.org WebGL] and [http://www.enable-javascript.com/ Javascript] compliant.		Check if your browser is [http://get.webgl.org WebGL] and [http://www.enable-javascript.com/ Javascript] compliant.

			If you prefer to run '''ACC''' on your own machine, possibly as part of much larger and more complex computational projects, a command line version of '''ACC''' is available. Its EEM, statistical and file conversion capabilities are the same as those of the '''ACC''' web server. Please read about how to use '''ACC''' in command line [[ChargeCalculator:CMD_Version \| here]].

	=Limitations and troubleshooting=		=Limitations and troubleshooting=

Crina: /* Structure */

2014-12-03T09:25:05Z

Structure

← Older revision		Revision as of 09:25, 3 December 2014
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	In order to produce chemically relevant atomic charges using EEM, it is necessary that the structure of the molecule be complete. No crucial parts should be missing. If parts of the structure are missing, appropriate cappings should be included. All protons should be present according to the relevant protonation state. Since '''ACC''' does not currently include functionality for editing the molecular structure, you must address these issues prior to uploading the molecule into '''ACC'''.		In order to produce chemically relevant atomic charges using EEM, it is necessary that the structure of the molecule be complete. No crucial parts should be missing. If parts of the structure are missing, appropriate cappings should be included. All protons should be present according to the relevant protonation state. Since '''ACC''' does not currently include functionality for editing the molecular structure, you must address these issues prior to uploading the molecule into '''ACC'''.

	'''ACC''' does check valences, and produces a ''missing H'' warning if they are not satisfied. Despite the warning though, '''ACC''' allows to proceed with the charge calculation step, as it might not always be possible to obtain a perfect structure (e.g., when working with low resolution structures of extremely large complexes). The results from such calculations may not have chemical meaning in their absolute values, but they can be very useful when comparing sets of charges (open vs closed conformation, free vs bound state, etc.).		'''ACC''' does check valences, and produces a <span style="color:#DAA520">''missing H'' warning</span> if they are not satisfied. Despite the warning though, '''ACC''' allows to proceed with the charge calculation step, as it might not always be possible to obtain a perfect structure (e.g., when working with low resolution structures of extremely large complexes). The results from such calculations may not have chemical meaning in their absolute values, but they can be very useful when comparing sets of charges (open vs closed conformation, free vs bound state, etc.).

	===Total charge===		===Total charge===

Crina: /* Parsing */

2014-12-03T09:12:35Z

Parsing

← Older revision		Revision as of 09:12, 3 December 2014
Line 38:		Line 38:
	'''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.

	Input files generally contain ''atom type'' information. Many different atom type schemes are used in different modeling projects. Moreover, many times the output is not even standardized between different applications implementing the same atom type scheme. '''ACC''' attempts to be a general utility, and currently implements only the detection of chemical elements. If the atom types in the input file differ from chemical elements, '''ACC''' will report them as ''unknown chemical elements'', and these atoms will be skipped during the EEM calculation (they will not contribute to the [[ChargeCalculator:Theoretical_background \| EEM matrix ]]). A similar problem will arise if the atom type information is not found at the expected place in the file. In the future, a more complex parsing algorithm may be implemented in '''ACC''' in order to cover the most common atom type schemes (e.g., AMBER, OPLS, etc.). Currently, the atom type parsing problem can be worked around either by uploading input files which adhere to the formal guidelines for their respective formats and contain atom types according to chemical elements, or by creating an EEM parameter set with special parameters for those atom types which '''ACC''' finds problematic.		Input files generally contain ''atom type'' information. Many different atom type schemes are used in different modeling projects. Moreover, many times the output is not even standardized between different applications implementing the same atom type scheme. '''ACC''' attempts to be a general utility, and currently implements only the detection of chemical elements. If the atom types in the input file differ from chemical elements, '''ACC''' will report them as <span style="color:#DAA520">''unknown chemical elements''</span>, and these atoms will be skipped during the EEM calculation (they will not contribute to the [[ChargeCalculator:Theoretical_background \| EEM matrix ]]). A similar problem will arise if the atom type information is not found at the expected place in the file. In the future, a more complex parsing algorithm may be implemented in '''ACC''' in order to cover the most common atom type schemes (e.g., AMBER, OPLS, etc.). Currently, the atom type parsing problem can be worked around either by uploading input files which adhere to the formal guidelines for their respective formats and contain atom types according to chemical elements, or by creating an EEM parameter set with special parameters for those atom types which '''ACC''' finds problematic.

	If the chain ID is not explicitly included in the input file, but the molecule contains multiple chains with overlapping residue serial numbers, the results will not be meaningful for the affected residues, and possibly even in the vicinity of these residues. '''ACC''' provides ''check chain ID'' warnings both before and after the computation if this problem is detected, so that the input file can be corrected.		If the chain ID is not explicitly included in the input file, but the molecule contains multiple chains with overlapping residue serial numbers, the results will not be meaningful for the affected residues, and possibly even in the vicinity of these residues. '''ACC''' provides <span style="color:#DAA520">''check chain ID'' warnings</span> both before and after the computation if this problem is detected, so that the input file can be corrected.

	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.

Crina: /* Structure */

2014-11-29T06:49:56Z

Structure

← Older revision		Revision as of 06:49, 29 November 2014
Line 28:		Line 28:

	===Structure===		===Structure===
	In order to produce chemically relevant atomic charges using EEM, it is necessary that the structure of the molecule be complete. No crucial parts should be missing. If parts of the structure are missing, appropriate cappings should be included. All protons should be present according to the relevant protonation state. Since '''ACC''' does not currently include functionality for editing the molecular structure, ~~thus~~ you must address these issues prior to uploading the molecule into '''ACC'''.		In order to produce chemically relevant atomic charges using EEM, it is necessary that the structure of the molecule be complete. No crucial parts should be missing. If parts of the structure are missing, appropriate cappings should be included. All protons should be present according to the relevant protonation state. Since '''ACC''' does not currently include functionality for editing the molecular structure, you must address these issues prior to uploading the molecule into '''ACC'''.

	'''ACC''' does check valences, and produces a ''missing H'' warning if they are not satisfied. Despite the warning though, '''ACC''' allows to proceed with the charge calculation step, as it might not always be possible to obtain a perfect structure (e.g., when working with low resolution structures of extremely large complexes). The results from such calculations may not have chemical meaning in their absolute values, but they can be very useful when comparing sets of charges (open vs closed conformation, free vs bound state, etc.).		'''ACC''' does check valences, and produces a ''missing H'' warning if they are not satisfied. Despite the warning though, '''ACC''' allows to proceed with the charge calculation step, as it might not always be possible to obtain a perfect structure (e.g., when working with low resolution structures of extremely large complexes). The results from such calculations may not have chemical meaning in their absolute values, but they can be very useful when comparing sets of charges (open vs closed conformation, free vs bound state, etc.).

	===Total charge===		===Total charge===

Crina: /* Parsing */

2014-11-29T06:49:08Z

Parsing

← Older revision		Revision as of 06:49, 29 November 2014
Line 36:		Line 36:

	===Parsing===		===Parsing===
	'''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~~. Failing to follow these guidelines may result in a few ....~~.		'''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.

	Input files generally contain ''atom type'' information. Many different atom type schemes are used in different modeling projects. Moreover, many times the output is not even standardized between different applications implementing the same atom type scheme. '''ACC''' attempts to be a general utility, and currently implements only the detection of chemical elements. If the atom types in the input file differ from chemical elements, '''ACC''' will report them as ''unknown chemical elements'', and these atoms will be skipped during the EEM calculation (they will not contribute to the [[ChargeCalculator:Theoretical_background \| EEM matrix ]]). A similar problem will arise if the atom type information is not found at the expected place in the file. In the future, a more complex parsing algorithm may be implemented in '''ACC''' in order to cover the most common atom type schemes (e.g., AMBER, OPLS, etc.). Currently, the atom type parsing problem can be worked around either by uploading input files which adhere to the formal guidelines for their respective formats and contain atom types according to chemical elements, or by creating an EEM parameter set with special parameters for those atom types which '''ACC''' finds problematic.		Input files generally contain ''atom type'' information. Many different atom type schemes are used in different modeling projects. Moreover, many times the output is not even standardized between different applications implementing the same atom type scheme. '''ACC''' attempts to be a general utility, and currently implements only the detection of chemical elements. If the atom types in the input file differ from chemical elements, '''ACC''' will report them as ''unknown chemical elements'', and these atoms will be skipped during the EEM calculation (they will not contribute to the [[ChargeCalculator:Theoretical_background \| EEM matrix ]]). A similar problem will arise if the atom type information is not found at the expected place in the file. In the future, a more complex parsing algorithm may be implemented in '''ACC''' in order to cover the most common atom type schemes (e.g., AMBER, OPLS, etc.). Currently, the atom type parsing problem can be worked around either by uploading input files which adhere to the formal guidelines for their respective formats and contain atom types according to chemical elements, or by creating an EEM parameter set with special parameters for those atom types which '''ACC''' finds problematic.

Crina at 03:34, 29 November 2014

2014-11-29T03:34:17Z

← Older revision		Revision as of 03:34, 29 November 2014
Line 7:		Line 7:
	Check if your browser is [http://get.webgl.org WebGL] and [http://www.enable-javascript.com/ Javascript] compliant.		Check if your browser is [http://get.webgl.org WebGL] and [http://www.enable-javascript.com/ Javascript] compliant.

	=Limitations=		=Limitations and troubleshooting=
	'''ACC''' implements the ''Electronegativity Equalization Method'' (EEM) for the calculation of atomic charges which respond to changes in the molecular conformation and chemical environment. The limitations of '''ACC''' can be intrinsic to EEM, or can be the result of the implementation itself.		'''ACC''' implements the ''Electronegativity Equalization Method'' (EEM) for the calculation of atomic charges which respond to changes in the molecular conformation and chemical environment. The limitations of '''ACC''' can be intrinsic to EEM, or can be the result of the implementation itself. We provide a description of these limitations, along with a few workarounds.

	==EEM related==		==EEM related==