Custom Probe(user-defined molecules) Molecules in DruGUI for Mixed-Solvent Simulations

[lllhh-x]

Dear Prody Developers, I am writing to inquire about the possibility of adding custom probe molecules (e.g., phenol, acetonitrile, or other small organic fragments) to mixed-solvent simulations in DruGUI.
Currently, DruGUI offers a set of default probes (e.g., -IPRO, -IMID, -ACTT), but I would like to incorporate user-defined molecules for druggability assessment. For example, I aim to simulate systems like:
bash
druggui mdm2.psf mdm2.pdb -IPRO 30 -IMID 30 -PHENOL 20 -ACETONITRILE 20
where -PHENOL and -ACETONITRILE are custom probes.
Questions:
Is it possible to add custom probes in the current DruGUI version?
If yes, could you provide guidelines on how to:
Prepare the topology (PSF) and parameter (PRM) files for new probes.
Integrate them into DruGUI’s workflow (e.g., modifying configuration files or scripts).
Thank you for your time and expertise. I greatly appreciate your work on this tool and look forward to your advice.

[anupam-banerjee]

Hi,

Unfortunately you cannot add your own probes (user-defined) using the present version of DruGUI. We are in the process of making that happen. You could access the list of all available probes from-
http://www.bahargroup.org/prody/tutorials/drugui_tutorial/cgenff.html
Hope this helps!