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-requ...@maillist.sys.kth.se> wrote:
>
> test=gmx.commandline_operation(executable = "pdb2gmx",
> arguments = ["-water", "spce"
> ,"-ff", "oplsaa"
> ]
> ...
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