Hi all,I wonder if anyone can help me work out what's going on here. I'm trying to convert a PDB file of ADP (from structure 3ATV) to mol2 format and add hydrogens. The first step seems to work fine:
babel -ipdb 3ATV_ADP.pdb -omol2 3ATV_ADP1.mol2 -p 7.4however as a check I thought I'd try to convert back from mol2 to PDB, but when I do I get lots of errors:
babel -imol2 3ATV_ADP1.mol2 -opdb tmp.pdb ============================== *** Open Babel Warning in Translate Cannot perform atom type translation: table cannot find requested types. ============================== *** Open Babel Warning in ReadMoleculeThis Mol2 file is non-standard. Cannot interpret atom types correctly, instead attempting to interpret as elements instead.
============================== *** Open Babel Warning in Translate Cannot perform atom type translation: table cannot find requested types. ============================== *** Open Babel Warning in Translate Cannot perform atom type translation: table cannot find requested types. ============================== *** Open Babel Warning in ReadMoleculeThis Mol2 file is non-standard. Cannot interpret atom types correctly, instead attempting to interpret as elements instead.
============================== *** Open Babel Warning in Translate Cannot perform atom type translation: table cannot find requested types. ============================== *** Open Babel Warning in Translate Cannot perform atom type translation: table cannot find requested types. ============================== *** Open Babel Warning in ReadMoleculeThis Mol2 file is non-standard. Cannot interpret atom types correctly, instead attempting to interpret as elements instead.
============================== *** Open Babel Warning in Translate Cannot perform atom type translation: table cannot find requested types. ============================== *** Open Babel Warning in Translate Cannot perform atom type translation: table cannot find requested types. ============================== *** Open Babel Warning in ReadMoleculeThis Mol2 file is non-standard. Cannot interpret atom types correctly, instead attempting to interpret as elements instead.
============================== *** Open Babel Warning in Translate Cannot perform atom type translation: table cannot find requested types. 1 molecule converted 12 warnings 11 audit log messagesThis seems to happen with versions 2.2.3, 2.3.0 and 2.3.1. Can anyone try to replicate this error? I have attached the PDB file. One interesting point is that if I leave out the -p option in the initial conversion I get 3 errors instead of 12. AutodockTools also chokes on the mol2 file created by OpenBabel. Presumably there is something wrong with the mol2 file, but I can't see what.
thanks a lot, Doug _____________________________________________________ Dr. Douglas R. Houston Lecturer Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
3ATV_ADP.pdb
Description: Protein Databank data
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