[gmx-users] pdb2gmx: Selecting Force Field in first command

[Justin Lemkul]

On 4/10/20 9:03 PM, fernando at hypernetlabs.io wrote:
> Hi all!
>
> Context
>
> I'm trying to run simple gromacs example commands below
>
> *	gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce
> *	gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter
> -water spc
>
>   
>
> In a Docker container with a Dockerfile (Dockerfile = instruction file for
> auto execution inside the container) containing the below:
>
>   
>
> FROM mariojmdavid/gromacs-cuda:2019.3-runtime <-- thanks Mario! :)
>
> WORKDIR /usr/local/gromacs
>
> COPY . /usr/local/gromacs
>
> ENTRYPOINT ["/usr/local/gromacs/bin/gmx","pdb2gmx", "-f", "1aki.pdb", "-o",
> "1aki_processed.gro", "-water", "spce"]
>
>   
>
> Problem
>
> Both simple examples ask to 'Select the Force Field' after the 1st command
> is executed. A Docker container is non-interactive so I can't really pass my
> option for Force Field after I send it off to auto-execute remotely.
>
>   
>
> Question
>
> Does anyone know how I can pass my Force Field selection from the start?

That's what the -ff flag does. See gmx help pdb2gmx for all command-line 
options.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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