> > I'm a PhD student. In my research, I'm using Obabel and have a problem > with this. After converting the molecules to physiological pH, deprotonated > molecules are not obtained in phosphate groups. >
I’m not sure if I understand. Basically, you want a tool that’s going to adjust protonation for all functional groups? That’s not what Open Babel does .. it has a set of rules, particularly for amino acids. At the moment, you may want to look at Dimorphite: https://github.com/durrantlab/dimorphite_dl/blob/master/README.md Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchisonlab.org/
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