>I have been trying to run some very simple structures to ensure that NBO is installed properly for my Firefly program (and to get familiar with using it). Trying to use acetaldehyde and DMSO as simple test cases I seem to be getting some errors that state that I have molecules too close together.
> **** THERE ARE ATOMS LESS THAN 0.100 APART, QUITTING... ****
The error message you're encountering suggests that there are atoms in your molecular structure that are too close together, specifically within a distance of 0.100 Å (angstroms). This can cause issues with the calculation and may lead to inaccurate or nonsensical results.
To resolve this issue, you need to adjust the geometry of your molecular structures to ensure that the atoms are appropriately spaced apart. Here are a few steps you can follow to resolve this problem:
1. Visualize your molecular structures: Use a molecular visualization software tool (e.g., Avogadro, VMD, PyMOL) to examine the geometry of your acetaldehyde and DMSO molecules. This will allow you to get a better understanding of how the atoms are positioned.
2. Identify and fix atom clashes: Look for regions where atoms are too close to each other, resulting in steric clashes. These clashes can occur when atoms are overlapping or are significantly closer together than the typical bond lengths for that element.
3. Adjust the bond lengths and angles: Use the visualization software to manually adjust the bond lengths and angles in your molecular structure. This involves stretching or compressing bonds and modifying the bond angles to ensure proper spacing between atoms.
4. Optimize the geometry: Once you have made the necessary adjustments, run a geometry optimization calculation. This will allow the molecular structure to relax and find the most stable configuration while satisfying the constraints you have set.
5. Check for atom overlaps again: After optimization, recheck your molecular structures to ensure there are no atom overlaps and that the atoms are appropriately spaced apart. You can also calculate bond distances to verify if they are within the expected range.
6. Retry your NBO calculation: Once you have resolved any atom clashes and obtained well-defined molecular structures, attempt running your NBO calculation again to check if the error message has been resolved.
By following these steps, you should be able to resolve the issue of atoms being too close together and successfully run NBO calculations for your acetaldehyde and DMSO molecules.