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

[fernando at hypernetlabs.io]

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?

 

Many thanks in advance!

Fernando