Hi Stuart, I have you tried removing the space between the "-p" flag and the value, like "-p7.4"?
Best, Miro -- Edelmiro Moman, PhD Department of Molecular Medicine Royal College of Surgeons in Ireland POSTAL ADDRESS: L5.08 Trinity Biomedical Sciences Institute - TBSI Trinity College Dublin 152 - 160 Pearse St Dublin 2 IRELAND Phone: +353 (0)1 896 3527 On 4 August 2016 at 22:00, Stuart <stuart.em...@reactionbiology.com> wrote: > 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 >
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