Update instructions for hydrogenation at pH 7

[naveenarun]

I noticed that the command obabel mymols.sdf -O outputfile.smi -p gives the wrong output, and should be obabel mymols.sdf -O outputfile.smi -p 7.4 instead.

[ghutchis]

Really? The default is 7.4. Can you give me an example on how the "wrong output" occurs?

[naveenarun]

Sure, here is the relevant info to reproduce. I used 5kh7.pdb (attached here as 5kh7.txt since Github restricts file types) and used the following two commands with their corresponding outputs:

obabel 5kh7.pdb -O 5kh7_nop.mol2 -p: gives 5kh7_nop.txt

obabel 5kh7.pdb -O 5kh7_withp.mol2 -p 7.4: gives 5kh7_withp.txt

The main difference is that the carboxyl group on 6T7 is protonated when -p is used but not when -p 7.4 is used. This can be verified using grep -c 'UNL16' *.mol2 in which an extra hydrogen is present in 5kh7_nop.mol2.

I tried doing a scan of number of hydrogens vs. pH using grep -c ' H ' *.mol2, it seems that -p corresponds to a pH of 0 in this case.