Hi all,I've been trying to convert the attached in.pdb file to .mol2 format. I happened to be using the -p option:
babel -ipdb in.pdb -omol2 out_p.mol2 -p 7.4 This produces a file that babel chokes on if used as input: babel -imol2 out_p.mol2 -opdb ============================== *** 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. Problem with molecule: in.pdb Cannot interpret atom types correctly, instead attempting to interpret atom type: C.cat1490 as elements instead.
============================== *** Open Babel Warning in Translate Cannot perform atom type translation: table cannot find requested types.Atom 1 in the mol2 file has been assigned as type C.cat, which presumably is causing the problem.
This atom is assigned type C.2 if I use the following command: babel -ipdb in.pdb -omol2 out_h.mol2 -h Is it that babel expects a space between the C.cat and the 1490?If so, that still doesn't explain why I get different atom type assignments using -p vs. -h. I know I can't use -p if I want the charges in the output to be sensible (I assign them separately later), but it's now looking like the -p option will also change atom types ...
Is it simply that the -p option is fully broken and I should just stop using it?
cheers, 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.
in.pdb
Description: Protein Databank data
out_p.mol2
Description: Binary data
out_h.mol2
Description: Binary data
------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
