Hi, Starting with your smiles, converting "outfile_noH.sdf" to "outfile_H.sdf" with the -p 7.4 option (or an other value) doesn't work for me either. It keeps running, like you said (Open Babel 2.3.2, Linux Ubuntu 14.04).
But with this compound with a double bond changed to a single bond, it works: CC1=C(C)C2=C(S1)N1C(NN=C1C)[C@H](CC(=O)OC(C)(C)C)N=C2C1=CC=C(Cl)C=C1 So I guess the unusual nitrogens cycle is involved somehow. Anyway, the compound should not be protonated at pH 7.4... :) Regards, Pascal 2016-08-05 19:28 GMT+02:00 Stuart Ember <stuart.em...@reactionbiology.com>: > Hi Geoff, > > > > I’m using Open Babel 2.3.2. on a Windows 10 system. > > > > Stuart > > > > *From:* Geoffrey Hutchison [mailto:geoff.hutchi...@gmail.com] > *Sent:* Friday, August 05, 2016 12:40 PM > *To:* Stuart Ember > *Cc:* Pascal Muller; babel > *Subject:* Re: [Open Babel] Command line help for protonation > > > > Can you or anyone else think of what the problem may be? > > > > No. It would certainly help if you gave more information on what platform > (OS) you're using and the version of Open Babel. > > > > -Geoff > > >
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