Thanks for the reply, the sdf file was actually produced from a smiles string using gen3d.
Best wishes, Scott On 12 March 2014 22:05, Geoffrey Hutchison <geoff.hutchi...@gmail.com>wrote: > 1. When converting a sdf file (see attached) for carbon monoxide to smi > format I get the following smi result: > > [C-]#[OH] > > > The SDF says it came through Open Babel.. presumably from some other > format. It gives formal charges: > M CHG 2 1 -1 2 1 > > This gives a -1 charge to the carbon and +1 to the oxygen: > Certainly the SMILES has an issue (why it protonated the oxygen) -- the > current development version gives: > [C-]#[O+] > > But I'm guessing you'd like a better SMILES for carbon monoxide. OK, but > the input is the issue. How/where did you get that SDF? > > > 2. Hydrogens are inserted when converting the smiles P#P for the > diphosphorus molecule to sdf format (see attached) using gen3d. > > > Indeed, there's clearly an issue with the valence for triple-bonded > phosphorous. There's no case for this in OB's atom typing, so it falls back > to an implicit valence of 3 (i.e., one connection to the P plus 2 > hydrogens). > > You can correct this by adding the following line to the atomtyp.txt file: > IMPVAL [$([#15]#*)] 1 # for P#P > > -Geoff >
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