I think you’re mixing up “obminimize” which is a specific tool, and
“obabel” which can convert, etc.
I’d suggest something like:
obabel {input_file} -O {output_file} -opdbqt --minimize -sd -ff GAFF -h
Best,
-Geoff
On Aug 8, 2023 at 2:24:21 PM, Lock Meister <meisterl...@gmail.com> wrote:
> Hi,
>
> I was trying to run Obminimize to convert SDF files that I converted from
> SMILE strings into PDBQT files, and when I run the code that I have to loop
> it with a perl script with multiple files, I'm constantly getting
> this error: "obminimize: cannot read input/output format!"
>
> I was wondering if there might be any reason for this as I'm not very
> experienced with coding or open babel, and have attached my code and an
> example .sdf file that I have. I'm on the most updated Open babel there is,
> and Ive made sure to correctly place the files in the respective folders.
>
> I was wondering maybe if there was anything that I'm doing wrong that you
> guys could point out that I've unsuccessfully been able to perform?
>
>
> Cheers,
> Locke
>
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