ChargeCalculator:FAQ: Difference between revisions
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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. 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. | ||
=After uploading my molecule, I | =After uploading my molecule, I got a warning about "unknown chemical element names". How will it affect my 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. '''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). | |||
'''ACC''' holds a predefined list of chemical elements from the periodic table of chemical elements. If '''ACC''' does not recognize the chemical element for an atom at the expected position in the input file, it will not include this atom in the atomic charge calculation because it cannot assign an atom type, and therefore EEM parameters. This means that the calculation will run only on the remaining atoms, and when you view the results the atomic charge value for the atoms with unknown chemical elements will be "NaN". If none of the chemical elements are recognized (e.g., the file format guidelines are not respected, or the input file comes from a modeling program which uses the element column to store its own atom types), you will get an error for the entire calculation. Finally, if the input file comes from a modeling program which uses the element column to store its own atom types, and these atom types overlap with known chemical elements, it is possible that '''ACC''' includes the atoms in the calculation, but it assigns wrong atom types. For example, if "Ca" appears in the element column and was originally meant as C-alpha, '''ACC''' will actually interpret it as calcium. | |||
You can circumvent these issues and make sure these atoms are included in the calculation correctly either by fixing the input file, or using a custom EEM parameter set. The first solution is to adjust the element column in the input file so that it really displays chemical elements. Additionally, make sure the input file follows the formal guidelines for its format. The second solution is to use an EEM parameter set in which you include EEM parameters for the atoms with unknown chemical elements. By doing so you actually define new atom types and corresponding EEM parameters. 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 ''unknown chemical element names''. 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 twice more into this new parameter set. Then change the ''Element'' tag in one case to "H1", and in the other to "Ho". Save the new set with a unique name, and 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. | |||
=I am getting an error about unknown chemical elements.= | =I am getting an error about unknown chemical elements.= | ||
Revision as of 20:55, 25 December 2014
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.
After uploading my molecule, I got a warning about "unknown chemical element names". How will it affect my 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. 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).
ACC holds a predefined list of chemical elements from the periodic table of chemical elements. If ACC does not recognize the chemical element for an atom at the expected position in the input file, it will not include this atom in the atomic charge calculation because it cannot assign an atom type, and therefore EEM parameters. This means that the calculation will run only on the remaining atoms, and when you view the results the atomic charge value for the atoms with unknown chemical elements will be "NaN". If none of the chemical elements are recognized (e.g., the file format guidelines are not respected, or the input file comes from a modeling program which uses the element column to store its own atom types), you will get an error for the entire calculation. Finally, if the input file comes from a modeling program which uses the element column to store its own atom types, and these atom types overlap with known chemical elements, it is possible that ACC includes the atoms in the calculation, but it assigns wrong atom types. For example, if "Ca" appears in the element column and was originally meant as C-alpha, ACC will actually interpret it as calcium.
You can circumvent these issues and make sure these atoms are included in the calculation correctly either by fixing the input file, or using a custom EEM parameter set. The first solution is to adjust the element column in the input file so that it really displays chemical elements. Additionally, make sure the input file follows the formal guidelines for its format. The second solution is to use an EEM parameter set in which you include EEM parameters for the atoms with unknown chemical elements. By doing so you actually define new atom types and corresponding EEM parameters. 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 unknown chemical element names. 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 twice more into this new parameter set. Then change the Element tag in one case to "H1", and in the other to "Ho". Save the new set with a unique name, and 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.
I am getting an error about unknown chemical elements.
I am not getting any charges...
I got a warning that some atoms were skipped...
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.