Python gmxapi.error

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1

GROMACS version:Version 2020
GROMACS modification: No
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Dear all,

I am trying to incorporate python in order to simplify my work, this is the code that I have written:

import gmxapi as gmx

traj_comp= open(‘traj_comp.xtc’, ‘r’)
rama_file = open(‘rama.xvg’,‘w’)

grompp = gmx.commandline_operation(executable =[‘gmx_mpi’], arguments =[‘rama’, ‘-f’,‘traj_comp’,’-o’, ‘rama_file’],
input_files ={’-f’: ‘traj_comp’}, output_files = {’-o’: ‘rama_file’})

grompp.run()

However this error comes up:

raise exceptions.ApiError(message) from e
gmxapi.exceptions.ApiError: Uncaught {} while providing output-publishing resources for {}.

What am I doing wrong and can someone enlighten me? Thank you very much.

Best,

Ben

2

In the script you provide, you define python variables traj_comp and rama_file, but you provide file arguments as the strings “traj_comp” and “rama_file”.

Also, you should not duplicate arguments in arguments and input_files / output_files.

I think what you intend is

grompp = gmx.commandline_operation(executable =[‘gmx_mpi’],
    arguments =[‘rama’],
    input_files ={’-f’: traj_comp}, output_files = {’-o’: rama_file})

The next version of the software provides more informative error messages, but I have filed https://gitlab.com/gromacs/gromacs/-/issues/3693 to specifically check for the input file existence.

3

Hi Eric,

Thank you very much, now it works. So you don’t need the ending like “.xtc” or “.mdp”?

Furthermore, I have extra questions:
If I want to

echo 15 | gmx genion -neutral yes -p

how do I write that in the python code?

Best,

Ben

4

So you don’t need the ending like “.xtc” or “.mdp”?

That depends on the tool. Some programs are sensitive to the suffix on the filename.

To be clear: In the example you gave you created a variable called rama_file and assigned to it a string value of “rama.xvg”.

To refer to the variable, you don’t use quotes.

rama_file is the variable.

'rama_file' is a typo.

For your other question, commandline_operation accepts a stdin key word argument in gmxapi 0.2. You would write

commandline_operation(‘gmx_mpi’,
    arguments=[‘genion', '-neutral', 'yes', '-p’],
    stdin='15')

gmxapi 0.2 is available pre-release in the master GROMACS branch and in the upcoming 2021 beta release, or from PyPI with the --pre flag to pip.
E.g.

pip install --upgrade "gmxapi>=0.2.0a1"
5

Thank you very much!

I tried to do that without the quotation mark, however that caused error in my code. With the ‘’, I can run it. Is it some error or am I not setting it up correctly?

Best,

Ben

6

Hi Eric,

Thanks for the help. I have no problem doing that with editconf, pdb2gmx etc commands. However, it seems like genion doesn’t work at all as you describe above. Do you have any idea? there is no error, it doesn’t produce a new out.gro file.

Best,

Ben

7

You were able to update to gmxapi 0.2 alpha okay? Note that the updated documentation is available at http://manual.gromacs.org/nightly/gmxapi/userguide/pythonreference.html

Can you please share an example script that you are having trouble with?

Also, check the erroroutput result.

I think I gave you incomplete advice. I think you will need to add at least one “newline” to the stdin.

Try

cmd = commandline_operation(
    ‘gmx_mpi’,
    arguments=[‘genion', '-neutral', 'yes', '-p’],
    stdin='15\n')
cmd.run()

or

cmd = commandline_operation(
    ‘gmx_mpi’,
    arguments=[‘genion', '-neutral', 'yes', '-p’],
    stdin='15\n\n')
cmd.run()

and maybe

if cmd.output.returncode.result() != 0:
    print(cmd.output.erroroutput.result())
8

Hi All,

I installed Gromacs with GMXAPI=ON but when I try to import gmx (import gmxapi as gmx) in python script it shows Module Error: No module name gmxapi

Upon following the tutorial (Full installation instructions — GROMACS 2022.2 documentation) it shows the errors. The summary of error is as follows

command errored out with exit status 1
Trying NInja generator
Trying Ninja generator  - failure
Error: failed building wheel for gmxapi

How to fix it?

PS: I have checked and found all required file are in place.

ls /path/to/gromacs/lib shows libgromacs and libgmxapi.
ls /path/to/gromacs/share/cmake/gmxapi shows several …cmake files.

Thanks

9

Hi @shivam1.

Your problem is unrelated to this thread.

Could you please post a new thread? You might describe the topic as “problem building gmxapi Python package”. Please include the commands that you typed and the complete output from the terminal. We need more information or we cannot diagnose the problem.