ChargeCalculator:FAQ - Revision history

Crina: /* How do I read the XML file with EEM parameters? */

2015-05-29T18:32:26Z

How do I read the XML file with EEM parameters?

← Older revision		Revision as of 18:32, 29 May 2015
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	Each EEM parameter set is marked by the ''ParameterSet'' tag and the attribute ''Name'', which encodes a unique identifier. Further, each EEM parameter set is described by properties marked by the ''Properties'' tag, which provide the literature reference and basic information about the development of the EEM parameters. Please read the section on [[ChargeCalculator:FAQ#How_do_I_choose_a_suitable_EEM_parameter_set.3F \| how to choose a suitable EEM parameter set]] in order to better understand the importance of the information given by ''Properties''.		Each EEM parameter set is marked by the ''ParameterSet'' tag and the attribute ''Name'', which encodes a unique identifier. Further, each EEM parameter set is described by properties marked by the ''Properties'' tag, which provide the literature reference and basic information about the development of the EEM parameters. Please read the section on [[ChargeCalculator:FAQ#How_do_I_choose_a_suitable_EEM_parameter_set.3F \| how to choose a suitable EEM parameter set]] in order to better understand the importance of the information given by ''Properties''.

	Next, the EEM parameters are given under the tag ''Parameters'', which has three attributes. ''Target'' and ''Priority'' are important for [[ChargeCalculator:FAQ#How_do_I_choose_a_suitable_EEM_parameter_set.3F \| choosing a suitable EEM parameter set]]. The attribute ''Kappa'' is actually a [[ChargeCalculator:Theoretical_background#EEM \| special EEM parameter]] which, conceptually, modulates the electrostatic interaction of each atom with the surrounding charges.		Next, the EEM parameters are given under the tag ''Parameters'', which has three attributes. ''Target'' and ''Priority'' are important for [[ChargeCalculator:FAQ#How_do_I_choose_a_suitable_EEM_parameter_set.3F \| choosing a suitable EEM parameter set]]. The attribute ''Kappa'' is actually a [[ChargeCalculator:Theoretical_background#EEM \| special EEM parameter]] which, conceptually, modulates the electrostatic interaction of each atom with the surrounding charges.

	<ParameterSet Name="~~E-NPA_6-31Gd_gas~~">		<ParameterSet Name="Bult2002_npa">
	<Properties>		<Properties>
	<Property Name="Author">~~Ionescu~~, C. M., ~~Geidl~~, S., ~~Svobodova Varekova~~, R., ~~Koca~~, J.</Property>		<Property Name="Author">Bultinck, P., Langenaeker, W., Lahorte, P., De Proft, F., Geerlings, P., Waroquier, M., Tollenaere, J. P.</Property>
	...		<Property Name="Publication">The Electronegativity Equalization Method II: Applicability of Different Atomic Charge schemes</Property>
	<Property Name="Priority">2</Property>		<Property Name="Journal">J. Phys. Chem. A, 106, 7895-7901</Property>
			<Property Name="Year">2002</Property>
			<Property Name="Target">Organic molecules</Property>
			<Property Name="QM Method">B3LYP</Property>
			<Property Name="Basis Set">6-31G*</Property>
			<Property Name="Population Analysis">NPA</Property>
			<Property Name="Training Set Size">138</Property>
			<Property Name="Data Source">Not Specified</Property>
			<Property Name="Priority">4</Property>
	</Properties>		</Properties>
	<Parameters Target="Atoms" Priority="0" Kappa="0.~~00700000~~">		<UnitConversion KappaFactor="0.529177249000" ABFactor="0.036749309000" />
			<Parameters Target="Atoms" Priority="0" Kappa="1.000000000000">
	<Element Name="C">		<Element Name="C">
	<Bond Type="1" A="2.~~46311000~~" B="0.~~00876600~~" />		<Bond Type="1" A="8.490000000000" B="18.300000000000" />
	<Bond Type="2" A="2.~~46311000~~" B="0.~~00876600~~" />		<Bond Type="2" A="8.490000000000" B="18.300000000000" />
			<Bond Type="3" A="8.490000000000" B="18.300000000000" />
	</Element>		</Element>
	<Element Name="H">		<Element Name="F">
	<Bond Type="1" A="2.~~45929400~~" B="0.~~01921200~~" />		<Bond Type="1" A="39.180000000000" B="88.200000000000" />
	</Element>		</Element>
	...		...
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	The actual [[ChargeCalculator:Theoretical_background#EEM \| EEM parameters]] are encoded in the attributes ''A'' and ''B'', conceptually related to electronegativity and hardness, respectively.		The actual [[ChargeCalculator:Theoretical_background#EEM \| EEM parameters]] are encoded in the attributes ''A'' and ''B'', conceptually related to electronegativity and hardness, respectively.

			Note also the ''Unit conversion'' tag used to unify the values of the parameters from different sources in literature. The attribute ''KappaFactor'' is the correction applied to the ''Kappa'' parameter, while the attribute ''ABFactor'' is the correction applied to the values of parameters ''A'' and ''B''. In the example above, the electronegativity and hardness and parameters (''A'' and ''B'', respectively) were originally given in eV, while the atomic distances were given in atomic units. '''ACC''' uses parameters ''A'' and ''B'' in relative units (Hartrees), and atomic distances in Angstroms. The conversion factors are:
			<pre>
			1 Hartree = 27.2114 eV
			1 atomic unit = 0.529177249 Angstroms
			</pre>
			Therefore, the following corrections will be applied to the EEM parameters. The ''Kappa'' parameter will be corrected by a ''KappaFactor'' of 0.529177249. The ''A'' and ''B'' parameters will be corrected by an ''ABFactor'' of 0.036749309 (1/27.2114).

	=How do I add EEM parameters if they do not exist?=		=How do I add EEM parameters if they do not exist?=

Crina: /* There are more NMR states (models) in my file. Can I run ACC on all, or just a few selected states? */

2015-05-29T18:11:10Z

There are more NMR states (models) in my file. Can I run ACC on all, or just a few selected states?

← Older revision		Revision as of 18:11, 29 May 2015
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	Therefore, if your input file contains more NMR states, you must first separate your initial file into multiple files, each containing a single NMR state of interest to you. Compress these files as .zip. Upload the .zip archive with all models into '''ACC''', and you can compute atomic charges for all models in a single '''ACC''' run.		Therefore, if your input file contains more NMR states, you must first separate your initial file into multiple files, each containing a single NMR state of interest to you. Compress these files as .zip. Upload the .zip archive with all models into '''ACC''', and you can compute atomic charges for all models in a single '''ACC''' run.

	For example, say you have a .pdb file containing 15 NMR models, and you wish to run '''ACC''' for models 1-5. Copy the records belonging to model 1 into a file called model1.pdb. Then the records belonging to model 2 into a file called model2.pdb~~. Continue till model 5~~, ~~either manually or via a script~~. Put these 5 files with unique names into a .zip archive, which you can then upload into '''ACC'''. Once you upload, you will see that '''ACC''' has detected each of the models separately.		For example, say you have a .pdb file containing 15 NMR models, and you wish to run '''ACC''' for models 1-5. Copy the records belonging to model 1 into a file called model1.pdb. Then the records belonging to model 2 into a file called model2.pdb, and so on. Put these 5 files with unique names into a .zip archive, which you can then upload into '''ACC'''. Once you upload, you will see that '''ACC''' has detected each of the models separately.

	=After uploading my molecule, I got a warning about "missing hydrogen atoms". How will it affect my calculation?=		=After uploading my molecule, I got a warning about "missing hydrogen atoms". How will it affect my calculation?=

Crina: /* The calculation ran, but I got a warning that some atoms were skipped. */

2015-03-03T22:21:51Z

The calculation ran, but I got a warning that some atoms were skipped.

← Older revision		Revision as of 22:21, 3 March 2015
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	EEM, the empirical approach used by '''ACC''' to calculate atomic charges, operates with atom types based on chemical elements. When uploading the input file, '''ACC''' needs to establish the chemical element of each atom, so that it can assign a suitable atom type, and subsequently EEM parameters. If '''ACC''' does not recognize the chemical element (see above why), or no EEM parameters are available for that chemical element, '''ACC''' cannot assign EEM parameters to that atom and it will thus be unable to include it in the EEM calculation.		EEM, the empirical approach used by '''ACC''' to calculate atomic charges, operates with atom types based on chemical elements. When uploading the input file, '''ACC''' needs to establish the chemical element of each atom, so that it can assign a suitable atom type, and subsequently EEM parameters. If '''ACC''' does not recognize the chemical element (see above why), or no EEM parameters are available for that chemical element, '''ACC''' cannot assign EEM parameters to that atom and it will thus be unable to include it in the EEM calculation.

	In the final results, the ~~atomic~~ charge for such atoms that are ''skipped'' will appear with the value "~~NaN~~". These values will not contribute to any of the statistics computed by '''ACC'''.		In the final results, the charge for such atoms that are ''skipped'' will appear with the value "n/a" in the web interface. In the downloadable results, the charge for these atoms will appear as 0.000 in the .mol2 and .pqr files, and as "-" in the .csv files. The .wprop files will not list these atoms at all. These values will not contribute to any of the statistics computed by '''ACC'''.

	=The calculation ran, but I did not obtain any charges.=		=The calculation ran, but I did not obtain any charges.=

Crina: /* Can I get good dipole moments? */

2014-12-30T20:56:38Z

Can I get good dipole moments?

← Older revision		Revision as of 20:56, 30 December 2014
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	Atomic charges are conceived to reflect the uneven distribution of electron density in the molecule. When employing atomic charges, you must be aware of the limitations inherent to the atomic point charge model. A single number can give an idea about whether there is more electron density around some atoms compared to others, but it cannot characterize the actual distribution of electron density in the space between the atomic nuclei. Thus, all properties which flow from this distribution are generally not well described using atomic charges.		Atomic charges are conceived to reflect the uneven distribution of electron density in the molecule. When employing atomic charges, you must be aware of the limitations inherent to the atomic point charge model. A single number can give an idea about whether there is more electron density around some atoms compared to others, but it cannot characterize the actual distribution of electron density in the space between the atomic nuclei. Thus, all properties which flow from this distribution are generally not well described using atomic charges.

	Dipoles and higher order multipoles are known to be poorly approximated by a point charge model. Dipole moments measure the degree of separation of positive and negative charge in the molecule (polarity), and are, by definition, very sensitive to small variations in the distribution of electron density. Even atomic charges computed at the quantum mechanical (QM) level have trouble reproducing dipole moments, though some ''charge definitions'' (see above) are less unsuccessful than others (MK charges can be satisfactory for estimating dipole moments for small molecules). It is thus clear that one cannot expect the accuracy of empirical models fitted to QM reference charges to ~~excede~~ the accuracy of QM atomic charges in reproducing dipole moments.		Dipoles and higher order multipoles are known to be poorly approximated by a point charge model. Dipole moments measure the degree of separation of positive and negative charge in the molecule (polarity), and are, by definition, very sensitive to small variations in the distribution of electron density. Even atomic charges computed at the quantum mechanical (QM) level have trouble reproducing dipole moments, though some ''charge definitions'' (see above) are less unsuccessful than others (MK charges can be satisfactory for estimating dipole moments for small molecules). It is thus clear that one cannot expect the accuracy of empirical models fitted to QM reference charges to exceed the accuracy of QM atomic charges in reproducing dipole moments.

	Nonetheless, it is not unlikely that you obtain reasonable results for relative dipole moments in series of derivatives of a certain chemical compound. In other words, the atomic charges obtained from '''ACC''' calculations may not provide accurate dipole moments for a single molecule, but it is possible to compare the polarities of many kinds of derivatives of this molecule. Note that the current implementation of '''ACC''' provides only the values of atomic charges, and you will have to compute the dipole moments yourself. In the future '''ACC''' might support such functionality.		Nonetheless, it is not unlikely that you obtain reasonable results for relative dipole moments in series of derivatives of a certain chemical compound. In other words, the atomic charges obtained from '''ACC''' calculations may not provide accurate dipole moments for a single molecule, but it is possible to compare the polarities of many kinds of derivatives of this molecule. Note that the current implementation of '''ACC''' provides only the values of atomic charges, and you will have to compute the dipole moments yourself. In the future '''ACC''' might support such functionality.

	'''Start by having a look at the main [[ChargeCalculator:Terminology \| terms]] used by ACC, or return to the [[ChargeCalculator:UserManual \| Table of contents]].'''		'''Start by having a look at the main [[ChargeCalculator:Terminology \| terms]] used by ACC, or return to the [[ChargeCalculator:UserManual \| Table of contents]].'''

Crina: /* Can I get good electrostatic potentials? */

2014-12-30T20:56:20Z

Can I get good electrostatic potentials?

← Older revision		Revision as of 20:56, 30 December 2014
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	Whether or not atomic charges can generate accurate electrostatic potentials depends on several factors. First, certain ''charge definitions'' (see above) are based on principles which relate atomic charges to electrostatic potentials. Therefore, if you expect to compute potentials based on the atomic charges, you should probably pick an EEM parameter set developed for a suitable ''charge definition'' (MK, CHELPG...). Second, the concept of atomic point charges is inherently limited with respect to describing charge gradients, therefore the resulting potentials in some areas of the 3D space around the molecule will be better described than in some other areas.		Whether or not atomic charges can generate accurate electrostatic potentials depends on several factors. First, certain ''charge definitions'' (see above) are based on principles which relate atomic charges to electrostatic potentials. Therefore, if you expect to compute potentials based on the atomic charges, you should probably pick an EEM parameter set developed for a suitable ''charge definition'' (MK, CHELPG...). Second, the concept of atomic point charges is inherently limited with respect to describing charge gradients, therefore the resulting potentials in some areas of the 3D space around the molecule will be better described than in some other areas.

	Further, one should keep in mind that EEM, the method used by '''ACC''' to calculate atomic charges, is an empirical approach. EEM parameters available in '''ACC''' were mostly fitted to reference data in the form of atomic charges from quantum mechanical (QM) calculations. EEM is an approximation meant to keep as much accuracy as possible (compared to reference data) while maximizing computational efficiency. Therefore, the maximum accuracy to be expected for EEM atomic charges cannot ~~excede~~ the accuracy of the corresponding QM charges in reproducing electrostatic potentials.		Further, one should keep in mind that EEM, the method used by '''ACC''' to calculate atomic charges, is an empirical approach. EEM parameters available in '''ACC''' were mostly fitted to reference data in the form of atomic charges from quantum mechanical (QM) calculations. EEM is an approximation meant to keep as much accuracy as possible (compared to reference data) while maximizing computational efficiency. Therefore, the maximum accuracy to be expected for EEM atomic charges cannot exceed the accuracy of the corresponding QM charges in reproducing electrostatic potentials.

	Finally, note that some papers provide straightforward evaluations of the ability of their EEM parameter sets to reproduce electrostatic potentials from QM calculations. So follow the citation of the EEM parameter set you plan to use, and see if this information is available in the original paper. Note that the current implementation of '''ACC''' provides only the values of atomic charges, and you will have to compute the electrostatic potentials yourself (e.g., on the [http://nbcr-222.ucsd.edu/pdb2pqr_1.8/ pdb2pqr server]). In the future '''ACC''' might support such functionality.		Finally, note that some papers provide straightforward evaluations of the ability of their EEM parameter sets to reproduce electrostatic potentials from QM calculations. So follow the citation of the EEM parameter set you plan to use, and see if this information is available in the original paper. Note that the current implementation of '''ACC''' provides only the values of atomic charges, and you will have to compute the electrostatic potentials yourself (e.g., on the [http://nbcr-222.ucsd.edu/pdb2pqr_1.8/ pdb2pqr server]). In the future '''ACC''' might support such functionality.

Crina: /* How do I add EEM parameters if they do not exist? */

2014-12-30T20:55:14Z

How do I add EEM parameters if they do not exist?

← Older revision		Revision as of 20:55, 30 December 2014
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	=How do I add EEM parameters if they do not exist?=		=How do I add EEM parameters if they do not exist?=

	EEM, the empirical approach used by '''ACC''' to calculate atomic charges, operates with atom types primarily based on chemical elements. When uploading the input file, '''ACC''' seeks to establish the chemical element of each atom, so that it can assign a suitable atom type, and subsequently EEM parameters. If '''ACC''' does not recognize the chemical element for an atom, it will report an <span style="color:#DAA520">''unknown chemical element name''</span> warning. If ACC recognizes the chemical element but cannot find any EEM parameters associated with it, it will report <span style="color:#DAA520">''Missing Atoms''</span>. Either way, '''ACC''' will not include this atom in the atomic charge calculation.		EEM, the empirical approach used by '''ACC''' to calculate atomic charges, operates with atom types primarily based on chemical elements. When uploading the input file, '''ACC''' seeks to establish the chemical element of each atom, so that it can assign a suitable atom type, and subsequently EEM parameters. If '''ACC''' does not recognize the chemical element for an atom, it will report an <span style="color:#DAA520">''unknown chemical element name''</span> warning. If '''ACC''' recognizes the chemical element but cannot find any EEM parameters associated with it, it will report <span style="color:#DAA520">''Missing Atoms''</span>. Either way, '''ACC''' will not include this atom in the atomic charge calculation.

	To make sure that even such problematic atoms are included in the calculation, you must use a custom EEM parameter set. At this point, if you have not done so till now, please have a look at [[ChargeCalculator:FAQ#How_do_I_read_the_XML_file_with_EEM_parameters.3F \| how to read the XML file with EEM parameters]] before you proceed.		To make sure that even such problematic atoms are included in the calculation, you must use a custom EEM parameter set. At this point, if you have not done so till now, please have a look at [[ChargeCalculator:FAQ#How_do_I_read_the_XML_file_with_EEM_parameters.3F \| how to read the XML file with EEM parameters]] before you proceed.

Crina: /* Why are the charges from different sets so different, and how are these differences relevant? */

2014-12-26T07:43:50Z

Why are the charges from different sets so different, and how are these differences relevant?

← Older revision		Revision as of 07:43, 26 December 2014
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	This fallback also happens when the input molecule contains an atom type with a maximum bond multiplicity which was indeed not covered during the development of the EEM parameters used in a given calculation. For instance, if the reference data used for the development of the particular EEM parameter set you chose did not contain any sp² nitrogen (''Bond Type''="2"), '''ACC''' will fall back to the EEM parameters for sp³ nitrogen (''Bond Type''="1"). '''ACC''' will produce a warning to inform you of this fact, and in the final results the atom type will still be N:2, as originally detected in the input file. It is up to you to decide if the values of atomic charges for these problematic atoms are acceptable.		This fallback also happens when the input molecule contains an atom type with a maximum bond multiplicity which was indeed not covered during the development of the EEM parameters used in a given calculation. For instance, if the reference data used for the development of the particular EEM parameter set you chose did not contain any sp² nitrogen (''Bond Type''="2"), '''ACC''' will fall back to the EEM parameters for sp³ nitrogen (''Bond Type''="1"). '''ACC''' will produce a warning to inform you of this fact, and in the final results the atom type will still be N:2, as originally detected in the input file. It is up to you to decide if the values of atomic charges for these problematic atoms are acceptable.

	=Why ~~are the charges from~~ different ~~sets so~~ different~~, and how are these differences relevant~~? =		=Why did different EEM parameter set produce different charges?=

	~~Explain charge definitions~~, QM reference data ~~and~~ EEM parameters...		EEM, the empirical method used by '''ACC''' to calculate atomic charges, relies on empirical parameters. Many EEM parameter sets have been developed using different reference data and fitting procedures.

			EEM parameters are generally developed based on reference quantum mechanical (QM) calculations. A QM calculation is characterized by the setup of the wave function calculation (theory level, basis set, environment), and the type of observables that will be calculated and interpreted. Most commonly, QM reference data used for the development of EEM parameters consists of atomic charges, which are derived from the observable electron density according to a specific ''charge definition'', meaning a procedure used to partition the molecular electron density, or to deduce the electrostatic contribution of each atom. Because atomic charges are not physical observables and have only a conceptual character, there is no unique ''charge definition'' that is universally accepted. Rather, a score of ''charge definitions'' have been published and are in use, each with their own strengths and weaknesses.

			We denote as ''approach'' any association of a QM calculation setup and ''charge definition''.

	{\| class="wikitable"		{\| class="wikitable"
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	\|'''Approach: QM Method, Basis Set, Population Analysis'''		\|'''Approach: QM Method, Basis Set, Population Analysis'''
	\|-		\|-
	\|''Description:'' ~~The~~ nature of the reference data used during the development of the parameters~~. Reference data generally comes from high level Quantum Mechanical (QM) calculations~~. The applicability domain of an EEM parameter set is closely related to the applicability domain of the reference QM data ~~used during the development~~.		\|''Description:'' association of a QM calculation setup and ''charge definition''. Gives the nature of the reference QM data used during the development of the EEM parameters. The applicability domain of an EEM parameter set is closely related to the applicability domain of the reference QM data.
	\|-		\|-
	\|''Possible values:''		\|''Possible values:''
	*''QM Method'' - level of theory used to solve Schrödinger's equation - HF, B3LYP, etc.		*''QM Method'' - level of theory used to solve Schrödinger's equation - HF, B3LYP, etc.
	''Basis Set'' - set of basis functions used to solve Schrödinger's equation - 6-31G, STO-3G, etc.		''Basis Set'' - set of basis functions used to solve Schrödinger's equation - 6-31G, STO-3G, etc.
	*''Population Analysis'' ~~defines how the reference data (most commonly atomic charges) were obtained~~ after solving Schrödinger's equation - MPA (Mulliken population analysis), NPA (Natural population analysis), MK (Merz-Kollman scheme for fitting to electrostatic potentials), etc.		*''Population Analysis'' - charge definition used after solving Schrödinger's equation to partition the molecular electron density, or to deduce the electrostatic contribution of each atom - MPA (Mulliken population analysis), NPA (Natural population analysis), MK (Merz-Kollman scheme for fitting to electrostatic potentials), etc.
			\|}

			Therefore, the first major factor which causes differences in charges is the ''charge definition'', or rather the inherently different principles used to define the amount of electron density to be assigned to each atom. The setup of the reference QM calculations may also cause differences, but much smaller than those caused by the ''charge definitions''. Note that such differences are to be expected, and can be quantified and analyzed in the '''Compare''' tab of the '''ACC Specifics page'''.

			Further, even when two EEM parameter sets were developed using the exact same ''approach'', they can still produce different sets of charges. The first reason is the size and nature of the training set that was used to produce the reference data. The training set, which is generally a set of molecules, actually defines the accessible parameter space. The second reason has to do with the parameter fitting procedure, which may have identified a completely different point in the parameter space even when the same training set was used.

			{\| class="wikitable"
			\|-
			\|'''Training Set Size, Data Source'''
			\|-
			\|''Description:'' Number and type of molecules used to produce reference data during the development of the EEM parameters.
	\|}		\|}

			Last but not least, the differences might be caused by an error in the parameters. If you detect such an error, please let us know, so that we may correct it.

	=Why do residues have non-integer charge?=		=Why do residues have non-integer charge?=

Crina: /* Can I combine EEM parameter sets? */

2014-12-26T07:22:19Z

Can I combine EEM parameter sets?

← Older revision		Revision as of 07:22, 26 December 2014
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	Note that you need not copy/paste content and make modifications as described here. You can directly use the XML form provided in the window which opens when you click the ''Add'' button, as long as you respect the XML syntax.		Note that you need not copy/paste content and make modifications as described here. You can directly use the XML form provided in the window which opens when you click the ''Add'' button, as long as you respect the XML syntax.

	=Can I combine EEM ~~parameter~~ sets?=		=Can I combine EEM parameters originating from different sets?=
	~~Say I~~ have a biomacromolecule ~~which binds~~ a drug ~~like molecule~~. ~~Not really~~ necessary (the parameters for ~~biomolecules seem good enough)~~. ~~Explain how~~ to ~~use~~ chemical elements ~~efficiently~~.
			Suppose you have a biomacromolecule in complex with a drug inhibitor. You may be wondering if it is necessary, or at least possible, to use different EEM parameter sets for the two molecules. From our experience, it is sufficient to employ a parameter set with the attribute ''target=biomolecules'' for the entire complex. Alternatively, you may want to use a certain set suitable for your type of molecule, but which misses EEM parameters for one atom type, and such parameters are available in a different set.

			If you really want to combine EEM parameters which originate from different sets, there is a way. In the input file, identify the chemical element column. For all atoms that you would like to treat differently, make some modification to the chemical element. This way, for example, the chemical elements of all ligand atoms can be changed from H, C, N, O, Cl into Hx, Cx, Nx, Ox and Clx. Then upload the molecule. '''ACC''' will report an <span style="color:#DAA520">''unknown chemical element names''</span> warning for the atoms whose chemical elements you have modified. All you need to do now is [[ChargeCalculator:FAQ#How_do_I_add_EEM_parameters_if_they_do_not_exist.3F \| create a custom parameter set]] as a copy of one parameter set, with additional ''Element'' tags from a second parameter set.

			It is very important to take note of the ''kappa'' parameter. It should be comparable in the two sets you want to merge. If this condition is not satisfied, you might have to alter the values of the new parameters before they can perform effectively with a different set. In general, when trying out such merges it is good to run a few parallel calculations in which you progressively change the value of the parameters in question, and inspect the resulting atomic charges. Try to look for intervals of the parameter space for which the trends in charges remain the same.

	=The calculation ran, but I got a warning that some atoms were skipped.=		=The calculation ran, but I got a warning that some atoms were skipped.=

Crina: /* How do I add EEM parameters if they do not exist? */

2014-12-26T06:59:15Z

How do I add EEM parameters if they do not exist?

← Older revision		Revision as of 06:59, 26 December 2014
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	=How do I add EEM parameters if they do not exist?=		=How do I add EEM parameters if they do not exist?=

	EEM, the empirical approach used by '''ACC''' to calculate atomic charges, operates with atom types primarily based on chemical elements. When uploading the input file, '''ACC''' seeks to establish the chemical element of each atom, so that it can assign a suitable atom type, and subsequently EEM parameters. If '''ACC''' does not recognize the chemical element for an atom, it will report an <span style="color:#DAA520">''unknown chemical element name'' ~~warning~~</span>. If ACC recognizes the chemical element but cannot find any EEM parameters associated with it, it will report <span style="color:#DAA520">''Missing Atoms'' ~~warnings~~</span>. Either way, '''ACC''' will not include this atom in the atomic charge calculation.		EEM, the empirical approach used by '''ACC''' to calculate atomic charges, operates with atom types primarily based on chemical elements. When uploading the input file, '''ACC''' seeks to establish the chemical element of each atom, so that it can assign a suitable atom type, and subsequently EEM parameters. If '''ACC''' does not recognize the chemical element for an atom, it will report an <span style="color:#DAA520">''unknown chemical element name''</span> warning. If ACC recognizes the chemical element but cannot find any EEM parameters associated with it, it will report <span style="color:#DAA520">''Missing Atoms''</span>. Either way, '''ACC''' will not include this atom in the atomic charge calculation.

	To make sure that even such problematic atoms are included in the calculation, you must use a custom EEM parameter set. ~~First~~, ~~in the table with EEM parameter sets~~, ~~click on one of the~~ [[ChargeCalculator:FAQ#~~How_do_I_choose_a_suitable_EEM_parameter_set~~.3F \| ~~suitable built-in parameter sets]] already available. Basic information about the set will be displayed in the panel~~ to the ~~right of the table. Then click the black ''View~~ XML~~'' button at the top of this panel~~ with ~~information. A new tab will open in your browser where the content of the~~ EEM parameter set will be displayed in XML format. Copy the content of this page, then return to the '''ACC Setup page'''. Click the black ''Add'' button on top of the table with parameter sets. A small window will open, where you select all the content (CTRL+A) and replace it with the content of the parameter set you ~~opened previously~~.		To make sure that even such problematic atoms are included in the calculation, you must use a custom EEM parameter set. At this point, if you have not done so till now, please have a look at [[ChargeCalculator:FAQ#How_do_I_read_the_XML_file_with_EEM_parameters.3F \| how to read the XML file with EEM parameters]] before you proceed.

	~~The idea is that you~~ will ~~need~~ to ~~actually define a~~ new ~~atom type~~ and ~~corresponding EEM parameters for~~ the ~~chemical element that is unknown or for which no EEM parameters are available~~.		First, in the table with EEM parameter sets, click on one of the [[ChargeCalculator:FAQ#How_do_I_choose_a_suitable_EEM_parameter_set.3F \| suitable built-in parameter sets]] already available. Basic information about the set will be displayed in the panel to the right of the table. Then click the black ''View XML'' button at the top of this panel with information. A new tab will open in your browser where the content of the EEM parameter set will be displayed in XML format. Copy the content of this page, then return to the '''ACC Setup page'''. Click the black ''Add'' button on top of the table with parameter sets. A small window will open, where you select all the content (CTRL+A) and replace it with the content of the parameter set you previously viewed and copied (CTRL+V).

	~~For example, say your input file contains hydrogen atoms identified~~ in ~~the element column as "H1" and "Ho", depending on their binding partner~~. ~~'''ACC'''~~ will ~~report them as <span style="color:#DAA520">''unknown chemical element names'' warnings</span>. You may create~~ a new EEM ~~parameter set based on one of~~ the ~~built-in sets already~~ available ~~in '''ACC'''~~ (~~see below how~~ to ~~do that)~~. Copy~~/paste~~ the ~~parameter information for hydrogen (all text enclosed in~~ the ''Element'' tags~~) twice more into~~ this ~~new parameter set. Then change~~ the ''~~Element name~~'' tag ~~in one case to "H1"~~, ~~and in the~~ other ~~to "Ho"~~. ~~Save~~ the ~~new set with a unique name and select it from~~ the ~~list~~. ~~When~~ you ~~start your computation,~~ the ~~atoms with the previously unknown element names "H1"~~ and ~~"Ho" will now be included in the calculation~~, ~~and treated by EEM parameters suitable~~ for ~~hydrogen~~.		You now have a copy of the built-in EEM parameter set. The idea is that you will need to actually define a new atom type and corresponding EEM parameters for the chemical element that is unknown or for which no EEM parameters are available. Pick a chemical element that has similar chemical properties (especially electronegativity and hardness) to the new chemical element you wish to introduce. Copy the whole content between the start and closing ''Element'' tags, and then paste this content inside the ''Parameters'' tag, but outside other ''Element'' tags. Now modify the attribute ''Name'' to the chemical element you wish to include. Then, inside each ''Bond'' tags, you will find the values for parameters ''A'' and ''B''. You may keep these values, or modify them. You may repeat this procedure for as many new chemical elements as you need.

	'''ACC''' ~~expects~~ to ~~find the chemical element at a pre-defined position in the input file, which depends on~~ the ~~formal guidelines established for each file format. For example, in .pdb files,~~ '''ACC''' ~~looks for~~ the chemical ~~element~~ in the ~~column after occupancy and temperature factor (positions 77-78)~~.		Save the new EEM parameter set with a unique name. '''ACC''' will validate the syntax and let you know if any further modifications are necessary. When you return to the '''ACC Setup page''', select your new parameter set from the table. When you start your computation, the atoms with previously unknown chemical elements or missing EEM parameters will now be included in the calculation, although the EEM parameters might not be optimal.

	~~Explain how to approximate parameters (e.g~~.~~, based on electronegaitivity)~~		Note that you need not copy/paste content and make modifications as described here. You can directly use the XML form provided in the window which opens when you click the ''Add'' button, as long as you respect the XML syntax.
	Add ~~procedure~~, ~~copy/paste~~.

	=Can I combine EEM parameter sets?=		=Can I combine EEM parameter sets?=

Crina: /* How do I add EEM parameters if they do not exist? */

2014-12-26T06:32:11Z

How do I add EEM parameters if they do not exist?

@@ Line 149: / Line 149: @@
 =How do I add EEM parameters if they do not exist?=
 Explain how to approximate parameters (e.g., based on electronegaitivity)
 Add procedure, copy/paste.