[Open Babel] Cleaning up structures

[Douglas Houston]

Hi all,

I'm having problems "cleaning up" the structure of a small molecule. I
was hoping to use obminimize to fix the distorted bond lengths/angles
in the nitro group of the attached file obmin_in.mol. However, the
program does not appear to be paying attention to the bond order
information in the .mol file - the output has lost the delocalisation
on both the nitro and carboxylate groups (see attached obmin_out.pdb).

The following command was used:
~/programs/openbabel-2.3.1/build/bin/obminimize -n 100 -imol
obmin_in.mol -opdb > obmin_out.pdb

This led me to try other input formats to obminimize in case it was a
problem with the way it reads .mol files. However, using babel to
convert the obmin_in.mol to say .mol2 format also loses the
delocalisation on the nitro and carboxylate groups; the corresponding


6  4  4  0  0  0  0
6  7  4  0  0  0  0

are changed to the following lines in the output (babel_out.mol2):

5     6     4    1
6     6     7    1

when in fact they should be:

5     6     4   ar
6     6     7   ar

or at the very least:

5     6     4    1
6     6     7    2

The command used was:

babel -imol obmin_in.mol -omol2 babel_out.mol2

Is there a problem with the way babel interprets .mol bond blocks?

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

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The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

lines in obmin_in.mol for the nitro group (note bond type 4 which denotes aromatic):

obmin_in.mol
Description: Binary data

obmin_out.pdb
Description: Protein Databank data

babel_out.mol2
Description: Binary data

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