As implying in the former email, check the charge and multiplicity you have to see whether they are reasonable.
> On Sep 23, 2017, at 4:36 PM, Rana Rehan Khalid <rrkhalid.umich.edu> wrote:
>
> Yes structure is broken how I can resolve this issue Sir.
>
> On Sep 24, 2017 2:25 AM, "Pengfei Li" <ambermailpengfei.gmail.com> wrote:
>
>> Hi Rana,
>>
>> The charge and multiplicity you choose may cause the structure broken
>> after QM optimization.
>>
>> Kind regards,
>> Pengfei
>>
>>> On Sep 23, 2017, at 12:05 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
>> wrote:
>>>
>>> Dear 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
>>> <bay_before_opt.png><bay_after_opt.png>________________
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Received on Sat Sep 23 2017 - 16:00:01 PDT
