ChargeCalculator:FAQ

What is the physical meaning of atomic charges?

Atomic charges, or atomic partial charges, are non-integer numbers quantifying the balance of positive (nuclear) charge and negative (electronic) charge associated with each atom. In the 3D space, atomic charges represent points placed at the position of the atomic nuclei, and may be termed atomic point charges. The molecular representation based on atomic point charges is thus a very basic abstraction of the molecular electron density.

Atomic charges are conceived to reflect the uneven distribution of electron density in the molecule. While atomic charges are merely concepts and not physical observables, they have been used heavily in theoretical and applied chemistry due to their highly intuitive character and correlation with measurable quantities such as the electrostatic potential, polarity, reactivity, etc. Nowadays, atomic charges are still integral parts of many modeling applications, and are still used in reasoning basic chemical processes.

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 (such as multipole moments) are generally not well described using atomic charges.

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

ACC can run on any number of molecules at a time, but each molecule must be uploaded in a separate file. Therefore, you must first separate your initial file into multiple files, each containing a single NMR state of interest to you. Archive 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.

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

Explain charge definitions, QM reference data and EEM parameters...

Why do residues have non-integer charge?

Why does the residue charge deviate from the formal values of -1 (negatively charged), 0 (neutral), +1 (positively charged)?

How do I choose the best parameter set?

Discussion above plus what to do with charges...

How do I add parameters if they do not exist?

Explain structure of the xml file; Explain how to approximate parameters (e.g., based on electronegaitivity) Add procedure, copy/paste.

Can I combine parameter sets if 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.

Can I get good electrostatic potentials?

Some papers report such. Also, some charges better than others...

Can I get dipole moments?

In general, no. The concept of atomic charges has its limitations. Dipoles and higher order multipoles are known to be poorly approximated by a point charge model. You may try though... maybe to compare the dipoles of derivatives of the same molecule...

How is EEM empirical, and how is it related to QM?

Start by having a look at the main terms used by ACC, or return to the Table of contents.