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For a system already loaded into memory, it is possible to assign quantum potentials—that is, to describe the entire system or a part of it using quantum chemistry (QC) methods. If the intention is to assign QC-type potentials to all atoms, simply click the "Quantum Chemistry" icon in the toolbar of the main window (see Figure 1). The highlighted color at the top of the window represents the reference color assigned to the selected system. When all atoms are added to the QC region (i.e., a fully quantum mechanical system), the text box indicating the number of atoms to be included will also display the tag "all".
Figura 1: Quantum Chemistry Window. The window also supports programs that connect with pDynamo3, such as xTB, ORCA and DFTB+.
The user must then correctly assign the value of the charge and multiplicity, as well as choose the method (level of theory) that he wants to apply to the system. If there is no error, the atoms now described by QC will be represented by Balls and Sticks, as showing in Figure 2 (default representation in Easyhybrid to represent atoms of this nature).
Before (only MM or undefined potentials)
After (only QC potentials)
Figure 2: When a group of atoms is described by QC potentials, they are represented by balls and sticks by EasyHybrid.
QC/MM Setup
When assigning QC potentials to only a subset of atoms while describing the rest of the system with molecular mechanics (MM), thereby creating a hybrid QC/MM system, it is first necessary to associate the system of interest with one of the force fields supported by pDynamo3.
Next, using the "Viewing Selection" mode, select the atoms of interest and designate them as part of the QC region. To do this, go to the "Selection" menu and choose "Set As QC Atoms," or access the same option from the selection menu in the GL area (Figure 3).
Select the atoms that should be in the QC region (in this case only one of the methyl groups of the alanine molecule was selected)
2. Click the right mouse button (mouse button 2) within the GL area. From the selection menu, choose the option "Set as QC Atoms".
A warning message may appear, indicating that a new QC region has been selected. Upon clicking "Yes", the QC method configuration window will pop up, allowing you to configure the QC method settings according to your requirements.
If all the information is correct and a new QC potential has been successfully assigned to the system using EasyHybrid, the software will represent the QC region in the form of balls and sticks.
Figura 3: Selection of a QC region in EasyHybrid. By default, the QC region is always represented in balls and sticks. This visual representation helps to distinguish the atoms within the QC region and provides a clear visualization of the hybrid QC/MM system
It is important to emphasize that the classic partial charges of the MM region, referring to the atoms that remain in the MM region, must be adjusted to ensure an integer sum. This adjustment is necessary for the convergence of calculations involving hybrid potentials. In cases where the sum of MM charges is not an integer value, the program does not allow the assignment of the chosen QC region.
In EasyHybrid, when selecting fragments of residues, such as a portion of the glutamic residue side chain (Figure 4), the program automatically rescales the charges of the remaining MM atoms within the residue. This rescaling process approximates the sum of the charges to the nearest integer, ensuring compatibility with the requirements for a hybrid system in pDynamo.
Select the atoms that should be in the QC region. In this case, we only have a part of the side chain of a glutamic acid. The charges of the remaining atoms in the amino acid do not add up to an integer. EasyHybrid will automatically correct them for you at the end of this process.
The total charge of the QC region is estimated by rounding the sum of the classical partial charges of the selected atoms. This value, along with the multiplicity, should be carefully inspected by the user.
A new "QC" region was assigned to the system containing only part of the side chain of the glutamic acid residue.
Figura 4: Selection of a QC region. In EasyHybrid, the rescaling of partial loads of fragmented waste by separating the QC and MM regions is done automatically.
Sometimes, when the program denies the assignment of a QC region, it is commonly due to problems with the partial charges in the MM region. In such cases, EasyHybrid offers a tool for inspecting and correcting charges if necessary.
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