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
Hi Marko,
I'm sorry for the confusion. The install instructions for gmxapi 0.1 on
GROMACS 2020 are at
http://manual.gromacs.org/current/gmxapi/userguide/install.html
I plan to update readthedocs in the next few days to cover both gmxapi
0.0.7 on GROMACS 2019 and gmxapi 0.1 (
