The bond orders may not have been guessed correctly. I suggest you open the
sdf in Avogadro (for example) and check the structure.
On Mon, 23 Aug 2021, 15:24 Kevin Skinner, wrote:
> I used Open Babel to convert an XYZ file to an SDF file. Both contained
> 27 atoms. After using confab, the outpu
I used Open Babel to convert an XYZ file to an SDF file. Both contained 27
atoms. After using confab, the outputs contain 28 atoms. I am not familiar
with SDF files, so do you have any suggestions as to where something might
be wrong?
- Kevin
On Mon, Aug 23, 2021 at 9:51 AM Noel O'Boyle wrote:
Which means that there is something wrong with your input. Or rather, your
input is not what you think it is. Take a look at that atom in the SDF and
see if you can figure it out.
Regards,
Noel
On Wed, 18 Aug 2021 at 22:25, Kevin Skinner wrote:
> Using an SDF file as the input did not correct t
Using an SDF file as the input did not correct the issue.
- Kevin
On Wed, Aug 18, 2021 at 5:17 PM Noel O'Boyle wrote:
> Ah OK. Try an sdf file, and then there will be no need for OB to guess
> anything.
>
> On Wed, 18 Aug 2021, 21:50 Kevin Skinner, wrote:
>
>> Hello,
>>
>> Thanks for the respo
Hello,
Thanks for the response. I already have all of the hydrogens that are
present in the structure. Confab is adding an extra hydrogen because it
thinks there should be one. Typically it does so in between, but over a
bond (like a triangle). Is there a sway to approach this? If not, then
would
Ah OK. Try an sdf file, and then there will be no need for OB to guess
anything.
On Wed, 18 Aug 2021, 21:50 Kevin Skinner, wrote:
> Hello,
>
> Thanks for the response. I already have all of the hydrogens that are
> present in the structure. Confab is adding an extra hydrogen because it
> thinks
Hi Kevin,
Working as intended. The forcefields and QM calculations require explicit
hydrogens to correctly calculate the energy. It's trivial to remove the H
afterwards, but this would be a bit unusual so think it over.
Regards,
Noel
On Wed, 18 Aug 2021 at 16:25, Kevin Skinner wrote:
> Hello,
Hello,
I am using confab to generate conformers, but while doing so it adds a
hydrogen to the structure. I have used the iQMol optimizer, PM3, and DFT
for the optimizations and all have the same issue. I have tried using both
XYZ and MOL2 inputs. Is there a way to avoid this issue?
Thanks,
Kevin
