Dear Paul, > how do I enable a "complete protonation" of all atoms within PyBEL?
Do you mean ionization? > A small > test of the OpenBabel Windows version revealed that COO- is converted COOH, > but R-NH2 is not converted to R-NH3+. > As data source, I work with MOL2 files, and this shall be the output as > well. > For the last group, the original atom type is set to N.3, and it is not > changed to N.4, although I chose a high pH of 14 to "protonate" the > molecule. Try a pH around 7 if you want both COO- and NH3+. In basic condition, amines are not protonated. echo "NCC(=O)O" | babel -i smi -p1 -o smi [NH3+]CC(=O)O (N.4 if mol2 outpout) echo "NCC(=O)O" | babel -i smi -p7 -o smi [NH3+]CC(=O)[O-] echo "NCC(=O)O" | babel -i smi -p14 -o smi NCC(=O)[O-] Regards, Pascal ------------------------------------------------------------------------------ Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
