[Chimera-users] Converting sdf file into mol2 format

[Eric Pettersen]

Hi Mahendra,
	Your coordinates are two-dimensional, not three-dimensional.  Chimera is not going to be able to correctly determine the atom types for a two-dimensional compound, nor appropriately protonate it, nor properly minimize it.    You could directly write a two-dimensional mol2 file from the sdf simply by dropping the runCommand("minimize") step of the processing script, but many of the mol2 atom types would be wrong.
	I think you need to use some other tool for your conversion.  Maybe Open Babel?

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Apr 29, 2015, at 11:01 AM, Mahendra B Thapa <thapamb at mail.uc.edu> wrote:

> Dear Chimera users,
> 
> I am trying to convert sdf file ( downloaded from diversity set data from 'http://scs.illinois.edu/htsf/compound_collection/nci.php') into mol2 format. When I ran the command chimera --nogui processSDF.py
> as given the previous posting ( http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004974.html), I got the following error messages:
> Cannot find consistent set of bond orders for ring system containing atom #0.73:1 at N1
> ---
> Unknown redo atom type: N3
> Traceback (most recent call last):
> 
> Any suggestions for correcting these errors will be a good help for me.
> 
> Thank you,
> Mahendra Thapa
> University of Cincinnati,OH
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