Dear OpenBabel community, 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...and running. Eventually, I just cancel the operation because nothing is done (well, a junk 28 k file is written that is not a real sdf). Am I entering the wrong syntax or somthing? I've even tried the above command minus the 7.4, but it still doesn't work. If someone can help with this command for the third step that would be great. Thanks. Stuart -- View this message in context: http://forums.openbabel.org/Command-line-help-for-protonation-tp4659417.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
