Hi Hetal,
As I always comment, "OB is not adding hydrogens. The hydrogens are already
there, just implicit." That is, your original MOL file is in fact Li(OH)2
(but you can't tell that unless you are familiar with the MOL file spec).
How are you creating the input file? Is there a way to set the valence? You
need to set the valence for the oxygens to force them to valence 1 (Roman
capital I), otherwise there's an implicit H.
Otherwise, just manually edit the file so that it looks something like:
3 2 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 Li 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 1 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 1 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
M END
Regards,
Noel
On Fri, 31 Mar 2023 at 15:43, Hetal Patel <hpa...@lbl.gov> wrote:
> Hi,
>
> I am trying to use minimization feature using uff but it is adding
> hydrogens to fill the shell. How do I prevent from addition of any
> additional atoms beyond what is in the input file.
>
> Here is a same input and the command I am using.
>
> Input.mol
>
>
>
>
> 3 2 0 0 0 0 0 0 0 0999 V2000
> 0.0000 -0.0000 -0.0000 Li 0 0 0 0 0 0 0 0 0 0 0 0
> 0.4622 -0.2286 -0.0600 O 0 0 0 0 0 0 0 0 0 0 0 0
> -0.4434 0.2193 0.0576 O 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0 0 0 0
> 1 3 1 0 0 0 0
> M END
>
> Command: obabel input.mol -O output.mol --minimize --steps 10000 --sd --ff
> uff
>
>
> output.mol:
>
>
> OpenBabel03302314253D
>
> 5 4 0 0 0 0 0 0 0 0999 V2000
> -0.0207 -0.0375 -0.0870 Li 0 0 0 0 0 0 0 0 0 0 0 0
> 1.7549 -0.3412 -0.5469 O 0 0 0 0 0 0 0 0 0 0 0 0
> -1.7957 0.2668 0.3744 O 0 0 0 0 0 0 0 0 0 0 0 0
> 2.2720 0.2359 0.0697 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.7870 0.3281 1.3627 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0 0 0 0
> 1 3 1 0 0 0 0
> 2 4 1 0 0 0 0
> 3 5 1 0 0 0 0
> M END
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