you can try this software https://openbabel.org/docs/dev/GUI/GUI.html

One of the easiest ways is using OpenBabel. Just upload your sdf file database and convert it to a desired format such as pdb or mol.

Do you have discovery studio software? If you have, you can open sdf file through it, and just save it as protein data bank (pdb) file.

You can do it using Open Babel software or an online web server available at https://cactus.nci.nih.gov/translate/

I want to add a question here. I'm using DS client to convert my sdf. files to pdb. Its pretty much easy but i want to know if i have to minimise or delete any bonds or add any charges (like to O-H) to the molecules before saving them in pdb format? My aim is to screen them to test whether they can pass through the blood-brain-barrier. Seeking advise from anyone who have done this before...

'Easy Convert' would be the best choice. It also supports batch conversion up to 1000 files.

OpenBabel is a great tool for this activity.

Dear all,

Here, I provided essential information for such conversion process with OpenBabel tool.

https://www.researchgate.net/post/How_to_convert_an_SDF_library_of_5000_molecules_to_individual_5000_mol_structure_files

Open Babel online tool

thanks

The sdf file can be uploaded on the online site cactus.nci.nih.gov/translate to convert the file to pdb.

Use Open Babel.

Download and install Open Babel software (https://sourceforge.net/projects/openbabel/ ), open the .sdf file in Openbabel GUI, select the output format, and then save it.

http://pasilla.health.unm.edu/tomcat/biocomp/convert

Dear Vasanth Bosco,

Hopefully, you have already found the solution to your question. Maybe, this would be helpful for future references.

It is also possible to use PyMol

This link may help:

https://www.youtube.com/watch?v=uobRSy5p1ZU&t=182s