[gmx-users] runtime error: pdb2gmx issues in Python API

[Eric Irrgang]

Hi Marko,

I apologize for the slow response.

"pdb2gmx" is not an executable, but an argument. Try

    gmx.commandline_operation(
        'gmx',
        ['pdb2gmx', '-water', 'spce', '-ff', 'oplsaa']
        ...)

I hope to be able to improve the documentation soon, but the exception
should have been more helpful. I have created issue #3376 at
https://redmine.gromacs.org/issues/3376

Best,
Eric

On Tue, Feb 4, 2020 at 5:55 PM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

>
>         test=gmx.commandline_operation(executable = "pdb2gmx",
>                                   arguments = ["-water", "spce"
>                                                ,"-ff", "oplsaa"
>                                                ]
> ...