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
Hi Rana,
First figure looks the molecule has two carboxylate. So you need to specify its total charge in executing antechamber (-nc -2) and G09 (-2 1).
Using Multiwfn (http://sobereva.com/multiwfn) to calculate RESP charges is more recommended. The procedure is much easier and the functionality is more powerful than Antechamber, and you do not need to boring with connectivity. Please follow the examples in Section 4.7.7 of Multiwfn manual.
- Badges
- Science topic