Hi,
> I am a new user and would like to use OpenBabel in order to perform the > following tasks on a small molecule (let's say the starting point is a > molecule represented as a smiles string). I'm having some difficulty with > the third step and would really appreciate some help from you veteran > Bablers out there. > > 1. Convert molecule from smiles to sdf format, with generation of 3D > co-ordinates. I can do this with the following command: > > obabel infile.smi -O outfile.sdf --gen3D > > 2. Remove all the hydrogens created during sdf generation: > > obabel outfile.sdf -O outfile_noH.sdf -d > > 3. Add hydrogens only present at pH 7.4: > > obabel outfile_noH.sdf -O outfile_H.sdf -p 7.4 > > When I enter the command above, nothing happens in the terminal and it just > keeps running These commands are working fine for me, starting with CCC(=O)O. Does this smiles fail for you too? What's your input smiles? Regards, Pascal
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