ADL: ADT problem

Cunningham, Phil phil.cunningham at
Wed Nov 2 05:04:19 PDT 2011

Hi Autodock

I have a pdb file I wish to convert to pdbqt format using ADT

I read in the molecule circa 4000 atoms

edit misc - check missing atoms  says 0 (zero)
edit hydrogens add polar only
edit charges add Kollman
edit charges compute Gasteiger - total charges added 6.0125
edit charges check totals on residues spread charge over all atoms

file write PDBQT  OK
ERROR Cannot create the PDBQT file, all atoms do not have an 
autodock_element field

can anyone point to my error?

both RasMol and Jmol can display / interact reasonably with the source file
babel / open babel blows up in windows and is taking an eternity on 
ubuntu (getting nowhere)

many thanks


Phil Cunningham
Senior Bioinformatics Officer
King's College London
Department of Biochemistry
Franklin Wilkins Building 3.157
150 Stamford Street
London W1 9NN
Tel +44 (0) 20 7848 4239

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