On browsing the Glide output, I noticed that whilst Glide has calculated Coulombic and polar terms, there are actually no partial charges in the files. Could you explain this?

The partial charges are stored in the output pose file (jobname_lib.maegz or jobname_pv.maegz), and they can be viewed in Maestro using the "Partial charge" option of the "Label atoms" toolbar button. However, the SD file format does not support atomic partial charges, only formal charges. So if you export or convert the Glide results to that format, you'll lose the partial charge information assigned during docking. This is the reason you wouldn't see partial charges when viewing the SD-converted results. If you need a non-Maestro file format that preserves these partial charges, you could use Mol2 instead of SD.

Keywords: partial charges, Glide output, Maestro, sdf file

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