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 - 14:30:03 PDT
