Hi

After getting the conformations as *.sdf (or *.pdb) files with
Macromodel (from Shroedinger) and/or Vconf(VeraChem) I use Chimera to
add missing H's and add charges with amber 99.
After these steps are completed, I split the sdf conformations-file
into single *.mol2 files. All works fine except for the last step,
that changes a single bond into a double bond in each molecule. I am
correcting this manualy opening the *.mol2 file with Texd editors and
changing the double bond into single bond the the benzene rings.
Opening a chosen conformation from the  *.sdf file it looks
correct.So, the problem happens during conversion/splitting process.

Question:
How can this  arbitrary bond change be avoided?


Attached zip file with *.mol2 examples of one compound after splitting  process.

Thank you
Regards
Bruno
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