How can I extract all molecules in an .sdf file and convert it as a .pdb file?

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Could you try using PeptiCloud and see if it's a useful tool for biology research?

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Bharath B.R

You can use dundees prodrg server.....

Http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg

Sergey Shityakov

Use the Autodock C-shell scripts for this conversion (mol2 to pdb). You can also convert your molecular data to the pdbqt files (pdb/mol2 to pdbqt).

Fortunatus Chidolue Ezebuo

See the attached document for how to use OpenBabel software

Bakary Ntji Diallo

Using OpenBabel at command line:

babel input.sdf output.pdb -m

Outputs will be numbered output1.pdb, output2.pdb, output3.pdb,

Blaine Mooers

Open babel (obabel) is the recommended replacement for babel. The following command works:

obabel nciList.sdf -O new.pdb -m

Hi Maryam Olagunju

You can try: obabel your.sdf -O dummy.pdb --split

Found here: https://sourceforge.net/p/openbabel/mailman/message/36089563/