ChargeCalculator:Technical details: Difference between revisions
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==EEM related== | ==EEM related== | ||
===Conformation dependence | ===Conformation dependence=== | ||
and in some conformation relevant for the | and in some conformation relevant for the maybe not suitable for all applications.. some require more general charges | ||
For instance, if the user produces an EEM model for the estimation of atomic charges compatible with certain force fields (e.g., GLYCAM for sugars which have not yet been included in its parameterization - gather more examples. AMBER???) | |||
=== | ===Parameters=== | ||
'''ACC''' relies on literature for the empirical parameters necessary during the EEM calculation. Not all atom types have been covered to date. For biomacromolecules and drug-like molecules, the most significant issue is posed by missing EEM parameters for P. Nonetheless, EEM is an ongoing topic of research in several labs, and it is expected that parameter sets with wider coverage will be available soon. | |||
For | |||
Until then, '''ACC''' provides the user with the opportunity to tune the available parameter sets by adding missing parameters or tweaking existing parameters according to their judgement. Running several calculations with slightly different parameters can provide an estimation of the expected error for a given biomolecular complex. | |||
. | |||
===Post-EEM methods=== | ===Post-EEM methods=== | ||
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===Total charge=== | ===Total charge=== | ||
The total molecular charge plays an important role in the quality of the '''ACC''' results, as it quantifies the amount of electron density that will be distributed across the molecule during the EEM calculation. The total molecular charge must be in tune with the protonation states. '''ACC''' assumes by default that all molecules are neutral, and it is the user's responsibility to mark the charged molecules with their correct total charge. | The total molecular charge plays an important role in the quality of the '''ACC''' results, as it quantifies the amount of electron density that will be distributed across the molecule during the EEM calculation. The total molecular charge must be in tune with the protonation states. '''ACC''' assumes by default that all molecules are neutral, and it is the user's responsibility to mark the charged molecules with their correct total charge. | ||
===Parsing=== | |||
Unknown elements due to bad parsing of atom types | |||
Assigning atom types based on bonds - may affect calculations using EEM parameter sets which distinguish between atom types based on types of bonds... | |||
Chain ID issue | |||
General parsing issue (must keep proper format) | |||
'''Return to the [[ChargeCalculator:UserManual | Table of contents]].''' | '''Return to the [[ChargeCalculator:UserManual | Table of contents]].''' | ||
Revision as of 02:30, 29 November 2014
Requirements
ACC is a free web service available online since June 2014 at http://ncbr.muni.cz/AtomicChargeCalculator. There is no login requirement for running ACC or accessing the results.
ACC runs on all modern browsers with JavaScript enabled. No further requirements exist for running ACC, or downloading and inspecting the results. For 3D visualization you will need an up to date internet browser with WebGL support.
Check if your browser is WebGL and Javascript compliant.
Limitations
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.
EEM related
Conformation dependence
and in some conformation relevant for the maybe not suitable for all applications.. some require more general charges
For instance, if the user produces an EEM model for the estimation of atomic charges compatible with certain force fields (e.g., GLYCAM for sugars which have not yet been included in its parameterization - gather more examples. AMBER???)
Parameters
ACC relies on literature for the empirical parameters necessary during the EEM calculation. Not all atom types have been covered to date. For biomacromolecules and drug-like molecules, the most significant issue is posed by missing EEM parameters for P. Nonetheless, EEM is an ongoing topic of research in several labs, and it is expected that parameter sets with wider coverage will be available soon.
Until then, ACC provides the user with the opportunity to tune the available parameter sets by adding missing parameters or tweaking existing parameters according to their judgement. Running several calculations with slightly different parameters can provide an estimation of the expected error for a given biomolecular complex.
Post-EEM methods
Several derivations of EEM (ABEEM, SFKEEM, SQEEM, etc.) have been published, which mainly aim to improve the ability of the post-EEM model to reproduce certain charge-derived ...dipoles, potentials... ACC currently implements only the classical EEM formalism, adjusted by Yang ... . The reason is that the classical formalism has a straightforward implementation, is ammenable to time and memory optimization techniques, and, most importantly, many EEM parameter sets are available for this formalism.
Implementation related
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.
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
The total molecular charge plays an important role in the quality of the ACC results, as it quantifies the amount of electron density that will be distributed across the molecule during the EEM calculation. The total molecular charge must be in tune with the protonation states. ACC assumes by default that all molecules are neutral, and it is the user's responsibility to mark the charged molecules with their correct total charge.
Parsing
Unknown elements due to bad parsing of atom types Assigning atom types based on bonds - may affect calculations using EEM parameter sets which distinguish between atom types based on types of bonds... Chain ID issue General parsing issue (must keep proper format)
Return to the Table of contents.