[Open Babel] mol2 format

[Chun T. <ta...@hh...>]

I have some questions about converting pdb format to tripos mol2
format.  To be honest, that I used openbabel is because the quote for
Tripos SYBYL  with only biopolymer module is close to seven thousand
dollars.  And all I need to do is to generate structure files in mol2
format, which are the input for software DOCK. I have noticed that the
mol2 file generated by openbabel does not have substructure and set
records. Also I want to know how different it is for the charge
assignment in the mol2 files generated from pdb files with or without
hydrogen atoms. Then I feeded the resulted mol2 file to grid, an
accessory program for DOCK. I got an error message:

Reading in coordinates of receptor.
WARNING read_mol2: Improper ATOM record substructure id for ***** in
mcdock.mol2.
Error reading in receptor.

Even after I added a fake substructure record in the mol2 file, I still
got the same error message.

Any suggestion is greatly appreciated.


Best,

Chun

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_.-=B7=B7-._.-=B7=B7-._.-=B7=B7-._.-=B7=B7-._.-=B7=B7-._.-=B7=B7-._.-
Chun Tang
Howard Hughes Medical Institute
University of Maryland, Baltimore County
1000 Hilltop Circle
Baltimore, MD 21250
Phone: (410)455-6347
Fax  : (410)455-1174