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

[Marko Petrovic]

I forgot to include my questions:
Questions:
- What is the cause python exception?
- Is there a more detailed documentation for gmx.commandline_operation() than gmxapi basic package<http://manual.gromacs.org/current/gmxapi/userguide/pythonreference.html#id1>


With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology

On 4 Feb 2020, at 15:53, Marko Petrovic <marko at kth.se<mailto:marko at kth.se>> wrote:

Hello

I'm trying to create a python implementation using the API of the entire lysozyme tutorial and have gotten stuck on the pdb2gmx step and can't decipher the error message nor figure out if my thinking is fundamentally wrong for this step. As can be seen in the code, I have tried to brute force my way to a solution as well.

        test=gmx.commandline_operation(executable = "pdb2gmx",
                                  arguments = ["-water", "spce"
                                               ,"-ff", "oplsaa"
                                               ]
                                               #,"-f",file_name
                                               #,"-o",out_name)
                                       ,
                                       #)
                                       input_files = {"-f":file_name},
                                       output_files = {"-o":out_name})
        test.run()


this gives the following error message as a result of a compound exception:
raise exceptions.ApiError(message) from e
gmxapi.exceptions.ApiError: Uncaught {} while providing output-publishing resources for {}.
Full error message included in attachment.

With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology
<errorlog.txt>
<P2_Lysozyme.py>