Removal of a charge in a sdf->mol2 conversion by molconvert

Good afternoon,

I apologize if i'm in the wrong part of the forum, this category seems the most appropriate for me to post my question, but I'm not quite sure it is.

In converting a molecule using molconvert, a charge seems to be missing on an oxygen (it does not appear in the MarvinViewer). I didn't use any kind of standardisation.

Here is the exact command: molconvert mol2 test.sdf > test.mol2

Is there a way and how can I prevent this behavior?

Please find the files of my example attached to this post.

Thanks.

 

Edit: I forgot to mention, I'm using JChem 5.4.

Thanks for the details. The calculated partial charges are stored for each atom which is ignored during import. This causes the incoherent behavior during export/import.

We will discuss this problem and get back to you soon.

Regards,

Gabor