Dear Pascal, what I want to obtain: Add all possible hydrogens, i.e. every N.3 becomes N.4, and every COO- becomes COOH.
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. (See attached file: b_noH.mol2)(See attached file: b_standardH.mol2) Is there a flag that I missed to process the MOL2 files in the preferred way? Cheers, Paul > Dear Paul, > > 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-] This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://disclaimer.merck.de to access the German, French, Spanish and Portuguese versions of this disclaimer.
b_noH.mol2
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b_standardH.mol2
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