CHARMM_GUI ERROR

[pablo-arantes]

CHARMM_GUI ERROR

[mdpoleto]

@TMoahanty this line below makes me think that you are not loading the force field files (toppar.str) to provide the parameters assigned to the topology specified at the .psf file.

Force Field files = ()

Can you double check if you actually defined the correct pathway for the toppar.str file? You can find more details about how to load it in the notebook itself.

[TMoahanty]

@mdpoleto Can you please let me know from where can I load the force field files. Can you please provide me the Link for loading the appropriate toppar.str file for protein stimulation ?

[mdpoleto]

@TMoahanty there is an entire section in the notebook explaining how to load the input files such as .psf, .crd and the toppar.str file. Note that if your toppar.str file was generated by CHARMM-GUI, you might need to fix the pathways for the force field files (.rtf, .prm and .str files) defined inside the toppar.str file. This is also mentioned in the notebook.

[TMoahanty]

@mdpoleto I am still facing some issues while executing the code:
CharmmFileError: [Errno 2] No such file or directory: '/content/drive/MyDrive/MDopen read card unit 10 name toppar/top_all36_prot.rtf'

[TMoahanty]

@mdpoleto Another error i faced while installing libraries:-
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
Traceback (most recent call last):
File "entry_point.py", line 76, in
File "tarfile.py", line 2036, in extractall
File "tarfile.py", line 2077, in extract
File "tarfile.py", line 2150, in _extract_member
File "tarfile.py", line 2199, in makefile
File "tarfile.py", line 247, in copyfileobj
File "tarfile.py", line 521, in read
File "tarfile.py", line 549, in _read
KeyboardInterrupt
[5366] Failed to execute script entry_point
concurrent.futures.process._RemoteTraceback:
'''
Traceback (most recent call last):
File "concurrent/futures/process.py", line 384, in wait_result_broken_or_wakeup
File "multiprocessing/connection.py", line 256, in recv
TypeError: init() missing 1 required positional argument: 'msg'
'''

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "entry_point.py", line 69, in
File "concurrent/futures/process.py", line 559, in _chain_from_iterable_of_lists
File "concurrent/futures/_base.py", line 608, in result_iterator
File "concurrent/futures/_base.py", line 445, in result
File "concurrent/futures/_base.py", line 390, in __get_result
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.
[5373] Failed to execute script entry_point

[pablo-arantes]

Hi @TMoahanty ,

Did you check the tutorial files (https://github.com/pablo-arantes/making-it-rain/tree/main/Colab_OpenMM_CHARMM)? There you can check how the files and pathways should be in your CHARMM-GUI outputs.
You should have in your Google Drive folder the following files: PSF, CRD, PDB, toppar.str and toppar folder (check the image below). Please, don't forget to put the correct pathway on Google_Drive_Path option in the notebook.
For example, if my folder on Google Drive is Pablo_MD, My pathway will be: /content/drive/MyDrive/Pablo_MD
Inside the Pablo_MD folder I should have all the files (PSF, CRD, PDB, toppar.str and toppar folder).

Regarding your second issue, this usually happens when you already have the libraries installed and is trying to install again. Just disconnect and connect again.

Thank you.

[TMoahanty]

Hi @pablo-arantes
Thank you so much for your guidance, I was able to run the above codes successfully.
But I faced some issues for which I request you to please guide me on that:-

1. How can I run 100 ns as right now I am able to run 2 ns per day?
2. Although I had run the MD production for 10 ns but before runtime was exhausted 2ns was completed but no file was created in my Drive till then. How can I save it ?
   Regards

[mdpoleto]

@TMoahanty please read our paper (https://chemrxiv.org/engage/chemrxiv/article-details/6116a01f424ea3ed758921a7) where we explain in details how to best explore the Colab runtimes. You have to calculate the number of strides you need to have to be able to finish at least one stride before your runtime is over. Again, all of this is explained in our paper and throughout the jupyter notebook.

[TMoahanty]

Hi @mdpoleto and @pablo-arantes !
Thank you so much for guidance as I have been able to run 18 ns production file till now. But while viewing the trajectory and PCA file I came across some error. So i request you to please guide on it.

ValueError Traceback (most recent call last)
/usr/local/lib/python3.7/dist-packages/matplotlib/axes/_axes.py in _parse_scatter_color_args(c, edgecolors, kwargs, xsize, get_next_color_func)
4238 try: # Is 'c' acceptable as PathCollection facecolors?
-> 4239 colors = mcolors.to_rgba_array(c)
4240 except ValueError:

9 frames
ValueError: Invalid RGBA argument: 0.0

During handling of the above exception, another exception occurred:

ValueError Traceback (most recent call last)
/usr/local/lib/python3.7/dist-packages/matplotlib/axes/_axes.py in _parse_scatter_color_args(c, edgecolors, kwargs, xsize, get_next_color_func)
4240 except ValueError:
4241 if not valid_shape:
-> 4242 raise invalid_shape_exception(c.size, xsize)
4243 # Both the mapping and the RGBA conversion failed: pretty
4244 # severe failure => one may appreciate a verbose feedback.

ValueError: 'c' argument has 36 elements, which is inconsistent with 'x' and 'y' with size 624.

[mdpoleto]

@TMoahanty you ran 18ns but you have only 9 frames being analyzed. That does not sound about right. Your errors seem to be from matplotlib, which is only plotting the PCA and not calculating it. Checking if your PCA calculation is indeed making an output file or array would be your first step.