Dear Amber + G09 Users

I use this command to prepare the .com input file for g09   

antechamber -i name.pdb -fi pdb -o bay.com -fo gcrt

for optimization this basis set and theory use in the route section

 #HF/6-31G* SCF=XQC Test Pop=MK iop(6/33=2) iop(6/42=6) opt

and simulation terminate normally. check point file and log file created. Then use these g09 output file for resp input file by using this command

antechamber -i bay.log -fi gout -o bay.mol2 -fo mol2 -c resp

this give following error

antechamber can only handle one unit.  If the input is a single unit

       then the connectivity is wrong and the geometry may be bad.

       Please convert your molecule to a mol2 file via:

       antechamber -j 5 -at sybyl -dr no

       And then check your molecule with a visualization program;

       manually add missing bonds or delete unwanted bonds as appropriate.

Then I opened the log file structure to visualize it. The structure break not look in its original given form. I also attached the images before opt and after opt. Due to this break of structure two unit show that cause antechamber error for RESP.

Kindly guide