Dear Pascal, Thanks you for your help. Steps 1 and 2 work fine (i.e. conversion of smiles to 3D-sdf, then removal of hydrogens), but step 3 still does not work. The smiles of the small molecule I am using is ‘CC1=C(SC2=C1C(=N[C@H](C3=NN=C(N32)C)CC(=O)OC(C)(C)C)C4=CC=C(C=C4)Cl)C’
Can you or anyone else think of what the problem may be? Stuart From: Pascal Muller [mailto:pascal.jm.mul...@gmail.com] Sent: Friday, August 05, 2016 4:21 AM To: Stuart Ember Cc: babel Subject: Re: [Open Babel] Command line help for protonation 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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