Dear Paul, > what I want to obtain: Add all possible hydrogens, i.e. every N.3 becomes > N.4, and every COO- becomes COOH.
Ok - let's use a acid pH of 1, then (option -p1). > For this purpose, I tried the following things: > "babel -imol2 b_noH.mol2 -pX -omol2 b_noH_out.mol2" > X was either 1, 7 or 14 > > I tried the same for the MOL2 file in which the hydrogens were already in > place for the non-polar atoms and the neutral nitrogen. > > Please find attached the corresponding MOL2 files. Both files generate the same mol2 file for me: babel -p1 b_noH.mol2 b_p1.mol2 (b_p1.mol2 attached) N.4 with 3 H, O.co2 converted in =O (O.2) and OH (O.3). If it's not the case for you, what's the output of echo "NCC(=O)O" | babel -i smi -p1 -o smi ? Check your OpenBabel version (should be 2.3.0) and be sure that there is only one version installed. By the way, I always use mol2 files with explicit hydrogens. Regards, Pascal
b_p1.mol2
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