Hi all,
I'm trying to find the quickest way to get ligands from the PDB website into
.mol2 format for use in another program.
The PDB website will let me download either the entire protein + ligand
complex as a .pdb file, or the ligand only in .sdf format.
I thought it would be quicker to download the ligands separately and convert
them from .sdf format to .mol2 format, but something weird happens when I do
that. If I run the OpenBabel program from command line, I get lots of
warning messages:
==============================
*** Open Babel Warning in Expand
Alias CL1 was not chemically interpreted
==============================
*** Open Babel Warning in Expand
Alias C2 was not chemically interpreted
==============================
*** Open Babel Warning in Expand
Alias C1 was not chemically interpreted
etc.
And then the output .mol2 file is missing all of the information about
chemical elements. They are all replaced with dummy atoms:
1 XX 6.3250 11.0900 22.6650 Du 1 LIG1 0.0000
2 XX 4.6490 11.0350 23.3060 Du 1 LIG1 0.0000
3 XX 4.0200 9.8040 23.4780 Du 1 LIG1 0.0000
etc.
The same loss of element information occurs if I run the iBabel graphical
interface, but it doesn't give me any warning messages. (Or any indication
that anything is even happening!).
I searched on Google and the Nabble site & couldn't find anyone else having
problems converting from .sdf to .mol2. I'm assuming there's something
"special" or "different" about the ligand .sdf files from the PDB website,
but I don't know what that is.
Any ideas?
I know that my other option is to chop up the .pdb files so that they only
contain the HETATM information, and then convert *that* to .mol2 - but I
only want to do that if it's going to be quicker than editing the
ligand-only .sdf files.
Thanks in advance,
helen-louise.
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