I just tried an example whereby I converted carazolol from sdf (from here:
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=71739&disopt=3DSaveSDF)
to mol2. Using the command:
babel -p 7 -isdf CID_71739.sdf -omol2 CID_71739
This assigns the non-aromatic nitrogen as an N.4 SYBYL atom type, meaning
nitrogen sp3 positively charged. However, the nitrogen is doubly protonated.
If I run a similar babel command:
babel -h -isdf CID_71739.sdf -omol2 CID_71739
The atom is also assigned as N.4, however the nitrogen is as expected
singly protonated.
Am I mistaken in thinking that the atom typing should change to N.3 in the
case where the -p 7 option is used?
Many thanks,
Jon
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