Thanks a lot for the advice! The structure I have is that of the small molecule bound to a protein. If I submitted this structure, without further geometry optimization, wouldn’t that overstabilize the bound ligand conformation?
I tried the geom=connectivity flag but it doesn’t work.
> Am 27.10.2017 um 21:20 schrieb David A Case <david.case.rutgers.edu>:
>
>> On Fri, Oct 27, 2017, Andreas Tosstorff wrote:
>>
>> I am trying to parametrize a ligand with antechamber and G16. However
>> the connectivity of my molecule is not as desired after running:
>>
>> antechamber -i IL3.mol2 -fi mol2 -o IL3.com -fo gcrt -gv 1 -ge IL3.gesp
>> -at gaff2
>>
>> and
>>
>> antechamber -i IL3.gesp -fi gesp -o IL3_resp.mol2 -fo mol2 -c resp -eq 2
>> -at gaff2
>>
>>
>> Specifically, a proton moves from a nitrogen to an oxygen, leading to a
>> COOH and NH2 instead of the desired COO- and NH3+.
>>
>> Is there a command to restrain the gaussian geometry optimization?
>
> Sure: edit the IL3.com file to remove the "opt" option from the route card,
> before running the Gaussian calculation. That will mean that you will use
> the starting configuration, so you will want to make sure that the geometry
> in the IL3.mol2 file is reasonable.
>
> ....dac
>
>
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Received on Sat Oct 28 2017 - 02:30:02 PDT
