ChargeCalculator:Motivation: Difference between revisions
No edit summary |
No edit summary |
||
| Line 2: | Line 2: | ||
Below you can find a few tips regarding the main applications of atomic charges in understanding and modeling the chemical behavior of molecules. This is by no means an exhaustive list, and ... | Below you can find a few tips regarding the main applications of atomic charges in understanding and modeling the chemical behavior of molecules. This is by no means an exhaustive list, and ... | ||
Be sure to also check out the Frequently Asked Questions section for additional information. | Be sure to also check out the [[ChargeCalculator:FAQ | Frequently Asked Questions]] section for additional information. | ||
=Understand and predict reactivity= | =Understand and predict reactivity= | ||
| Line 20: | Line 20: | ||
=Molecular Mechanics simulations= | =Molecular Mechanics simulations= | ||
explain FF compatibility | explain FF compatibility | ||
ACC does not provide input files specific to each simulation package, mainly because there are too many of them. | Currently, '''ACC''' does not provide input files specific to each simulation package, mainly because there are too many of them, each different and continuously evolving. However, ACC provides molecular structure files containing charges (mol2, pqr), as well as files containing only charges (.mchrg) which can be easily incorporated in other file formats. | ||
'''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]].''' | ||
Revision as of 19:34, 24 December 2014
However, What one can do with atomic charges strongly depends on the nature of the charges. Below you can find a few tips regarding the main applications of atomic charges in understanding and modeling the chemical behavior of molecules. This is by no means an exhaustive list, and ...
Be sure to also check out the Frequently Asked Questions section for additional information.
Understand and predict reactivity
Atomic or residue level
Analyze charge transfer pathways
While the absolute values of atomic charges cannot be validated experimentally, and even when they themselves do not correlate with any phenomenon observable for a certain molecular system under given conditions available to the user (or in literature), it is possible that the relative differces in charges hold further information about chemical reactivity and biological significance. Given two states of the same system, calculate the charges, look for patterns - atoms, residues or other types of molecular fragments (e.g., multiple water molecules in the binding site) for which the charge varies significantly between the two states.
Quantitative Structure-Property Relationships modelling
QSPR for various properties - pharmacokinetics... pKa example? Atomic charges can be used as descriptors, generally in combination with various other descriptors (based on the molecular topology, 3D structure, electronic structure, etc.)
Generating molecular conformations
Docking
Molecular Mechanics simulations
explain FF compatibility Currently, ACC does not provide input files specific to each simulation package, mainly because there are too many of them, each different and continuously evolving. However, ACC provides molecular structure files containing charges (mol2, pqr), as well as files containing only charges (.mchrg) which can be easily incorporated in other file formats.
Start by having a look at the main terms used by ACC, or return to the Table of contents.