PDB file using GAUSSIAN 16 optimization

[chmenaive]

TL;DR Summary

PDB files for docking( gaussian 16 - DFT optimization)

Hello There,

I am studying docking of ligand molecules into DNA using Autodock Vina. Before doing that I optimize the ligand molecule using Gaussian 16. I want to know how can we get the PDB format after optimization. Do I just need to open the .chk file and save it as PDB format or do I need to do some additional steps to convert it into PDB format after optimization. I will appreciate if you can please guide.

Thank you for your time.

 

[jbsteele]

To get the PDB format after optimization, you can use the Gaussian 16 Conversion utility which is available for free download. This utility can convert the .chk file into a PDB format. You will need to open the .chk file in this utility and save the file as a PDB format. Alternatively, you can also use other online tools such as OpenBabel to convert the .chk file into a PDB format. All you need to do is upload the .chk file on the tool and select the output format as PDB. I hope this information helps.