ADL: Ligand preparation

mf536 at york.ac.uk mf536 at york.ac.uk
Tue Mar 4 11:00:49 PST 2008


Oh dear,

I prepared individual ligand pdb-files from a multiple sdf-file (using 
babel) then trying to convert them into using the prepare_ligand4.py 
script.

That works fine for most of the ligands apart from - an error that 
parameters for N could not be generated which is surprising because other 
files containing N have been converted successfully - and a meaningless 
connectivity when looked at in adt afterwards (even for ligands where no 
error was detected)
   
Any ideas?

Thanks a lot,
Marcus

_________________it says___________________ Unable to assign MAP type to 
atom N Sorry, there are no Gasteiger parameters available for atom 
compound: :UNK1:N Unable to assign MAP type to atom N Sorry, there are no 
Gasteiger parameters available for atom compound: :UNK1:N Unable to assign 
MAP type to atom N Sorry, there are no Gasteiger parameters available for 
atom compound: :UNK1:N Sorry, there are no Gasteiger parameters available 
for atom compound: :UNK1:O Unable to assign XYZ type to atom N Unable to 
assign XYZ type to atom N Unable to assign XYZ type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign XYZ type to atom N Unable to 
assign XYZ type to atom N Unable to assign XYZ type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign XYZ type to atom N Unable to 
assign XYZ type to atom N Unable to assign XYZ type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N Unable to assign HYB type to atom N Unable to 
assign HYB type to atom N



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