User 8c57fe7217
14-10-2010 20:02:16
If I create a compound with nitro groups in Marvin Sketch and save it as a mol2 file, when the file is reopened, the nitro groups are no longer shown correctly (i.e., with a double bond to one O atom, a single bond to the other O atom, a negative charge on one O atom and a positive charge on the N atom). Instead, the nitro group now has the single-bonded O atom with a hydrogen attached, HO-N=O. Is this a bug? If not, is there a way to correct this behavior? Thank you.
ChemAxon 8b644e6bf4
22-10-2010 18:38:19
Dear Rudy,
Thanks for the bug report and sorry for the late answer. The calculated partial charges are saved to the mol2 file instead of the specified formal charge. As a workaround you can edit the mol file by writing "1.0000" and "-1.0000" to the appropriate atoms charge field. See attached example.
We will discuss our possibilities about this problem and get back to you soon.
Regards,
Gabor
ChemAxon d51151248d
03-11-2012 09:38:05
Dear Rudy !
The bug is already corrected. Nitro compounds saved as a .mol2 format are rendered correctly.
I made a test with Marvin 5.10 and 5.11.
Daniel
User 8c57fe7217
03-11-2012 14:18:11
Dear Daniel,
Thank you for your reply. I find if I draw 1,3-dinitrobenzene and save it as a mol2 file, when I reopen the file in MarvinSketch 5.11.3 (on Mac 10.8.2), the nitro groups are still not rendered correctly. However, if I save the structure as an sdf file, when I reopen the file the structure is rendered correctly. This procedure is working sufficiently well for me that I would consider the issue solved.