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 - 15:00:04 PDT
