Re: [Open Babel] obminimize outputs only in pdb (multimolecule pdb)

Hi Geoff, When I tried to convert a multimolecule pdb file (output from obminimize) to an sdf file, only the first molecule was converted. I wrote my own script to split the file into multiple pdbs and put them together as single sdf using obabel. But any solution using obabel to that in single

Re: [Open Babel] obminimize outputs only in pdb (multimolecule pdb)

Thanks. I will try that. Sundar Thangapandian > On Oct 19, 2017, at 6:40 PM, Geoffrey Hutchison > wrote: > > The obminimize program does not have all the features of the obabel command. > You can naturally convert a PDB file to SDF: > > obabel file.pdb -O file.sdf

Re: [Open Babel] obminimize outputs only in pdb (multimolecule pdb)

The obminimize program does not have all the features of the obabel command. You can naturally convert a PDB file to SDF: obabel file.pdb -O file.sdf > I tried -osdf filename.sdf and it didn't work. How can I get it in sdf format? > Or how can I convert multimolecule pdb file to an sdf file?

[Open Babel] obminimize outputs only in pdb (multimolecule pdb)

Hi, obminimize outputs only in pdb format. I tried -osdf filename.sdf and it didn't work. How can I get it in sdf format? Or how can I convert multimolecule pdb file to an sdf file? Thanks, Sundar -- Check out the