you can perform it on linux terminal, if you have windows then download ubuntu and open terminal and go to your directory, then perform

1. obminimize -ff MMFF94 -sd source.sdf > target.sdf

2. obabel -isdf target.sdf -osdf -O *.sdf -m

3. obabel target.sdf -O out.sdf --gen3d

4. obabel *.sdf -O *.pdbqt -m

these steps will minimize, split and save it into pdbqt format.

Thank you so much Kavita Patel .

I executed the command obminimize -ff MMFF94 -sd file.sdf > target.sdf.

The command ran successfully for a while but eventually terminated with an error message stating,

'SETTING UP BOND CALCULATIONS... COULD NOT FIND PARAMETERS FOR BOND 1-2 (IDX)... obminimize.exe: could not set up force field.'

What might have caused this issue?

Thanks in advance.

can you copy and paste the whole error?

Yeah sure.

This is the whole error statement I encountered,

"S E T T I N G U P C A L C U L A T I O N S

SETTING UP BOND CALCULATIONS...

COULD NOT FIND PARAMETERS FOR BOND 1-4 (IDX)...

obminimize: could not setup force field."

Also, is there any way to determine up to which molecule the command ran successfully?

Thank you again!

I think there is a problem with your ligand's geometry. the SDF file which has provided by that database has given wrong parameters or missing parameters, I suggest you try a different database.

There is a Tool for minimization of multiple molecules. Email me on [email protected]