"skipped empty mol2 file" typically indicates that the program encountered an issue with the input files during the generation of the PDB file in CHARMM-GUI Solution Builder. Reasons and troubleshooting steps to try:

1. Check the input files: Ensure that the input files (.mol2 files) are not empty and contain valid molecular structure information. You can open the .mol2 files with a text editor to verify their contents.

2. Verify the file formats: Confirm that the .mol2 files are in the correct format and adhere to the specifications required by CHARMM-GUI Solution Builder. The files should include the necessary sections such as "@MOLECULE" and "@ATOM" with appropriate molecular and atom information.

3. Validate the input files: If you suspect any issues with the .mol2 files, you can try validating them using external tools or online validators. There are various online resources available that can check the integrity and correctness of the .mol2 file format.

4. Regenerate the .mol2 files: If the input .mol2 files are generated using external tools like OpenBabel or sort_mol2_bonds.pl, try regenerating them using different settings or approaches. It's possible that the previous generation process introduced some errors or inconsistencies in the files.

5. Check for any special characters or file encoding issues: Ensure that there are no special characters or unexpected file encoding issues present in the .mol2 files. Special characters or incompatible encodings can cause parsing errors during the PDB generation process.

6. Contact CHARMM-GUI support: If the issue persists despite trying the above steps, it may be helpful to reach out to the support team of CHARMM-GUI. They can provide specific guidance or troubleshoot any potential bugs or technical issues related to the Solution Builder module.

Hope it helps