Issue converting CG dcd to all atom dcd using the "Martini+cg2all.ipynb"

[kabirbiswas]

Really appreciate your efforts towards to writing all the colab notebooks.

While running the , I encountered the following error during conversion of the CG dcd to all atom dcd using the "Martini+cg2all.ipynb". Would you please suggest any specific changes to the notebook for getting this step to work? Note that script suggestions by Google Gemini did not work.

Error text:

CalledProcessError Traceback (most recent call last)

in <cell line: 1>()
----> 1 get_ipython().run_cell_magic('bash', '', '\nmamba activate cg2all\npython\nimport cg2all.lib.libmodel\nfrom cg2all.lib.libconfig import MODEL_HOME\nfor model_type in ["Martini", "Martini3",]:\n ckpt_fn = MODEL_HOME / f"{model_type}.ckpt"\n if not ckpt_fn.exists():\n cg2all.lib.libmodel.download_ckpt_file(model_type, ckpt_fn)\n\nimport os\nimport subprocess\nimport sys\n\nGoogle_Drive_Path = '/content/drive/MyDrive/CG-MD-sim/mNG-flex-NLuc-02' #@param {type:"string"}\nworkDir = Google_Drive_Path\nJobname = "mNG-flex-NLuc" #@param {type: "string"}\n\nCoarse_grained_model = "Martini3" #@param ["Martini", "Martini3"]\n\nbatch_size = 1 #@param {type: "number"}\n#@markdown - Batch size should be a divisor of the total number of frames.\n# device = "cuda" #@param ["cpu", "cuda"]\n\ntraj_input = os.path.join(workDir, str(Jobname) + "_cg_nw.dcd")\npdb_input = os.path.join(workDir, str(Jobname) + "_nw.pdb")\npdb_ini_output = os.path.join(workDir, str(Jobname) + "_frame0_backmapped.pdb")\ntraj_output = os.path.join(workDir, str(Jobname) + "_backmapped.dcd")\npdb_output = os.path.join(workDir, str(Jobname) + "_backmapped.pdb")\nbackmap_align_dcd = os.path.join(workDir, str(Jobname) + "_backmapped_align.dcd")\nbackmap_align_pdb = os.path.join(workDir, str(Jobname) + "_backmapped_align.pdb")\n\nsubprocess.run("convert_cg2all -p " + str(...

4 frames

in shebang(self, line, cell)

/usr/local/lib/python3.10/dist-packages/IPython/core/magics/script.py in shebang(self, line, cell)
243 sys.stderr.flush()
244 if args.raise_error and p.returncode!=0:
--> 245 raise CalledProcessError(p.returncode, cell, output=out, stderr=err)
246
247 def _run_script(self, p, cell, to_close):

CalledProcessError: Command 'b'\nmamba activate cg2all\npython\nimport cg2all.lib.libmodel\nfrom cg2all.lib.libconfig import MODEL_HOME\nfor model_type in ["Martini", "Martini3",]:\n ckpt_fn = MODEL_HOME / f"{model_type}.ckpt"\n if not ckpt_fn.exists():\n cg2all.lib.libmodel.download_ckpt_file(model_type, ckpt_fn)\n\nimport os\nimport subprocess\nimport sys\n\nGoogle_Drive_Path = '/content/drive/MyDrive/CG-MD-sim/mNG-flex-NLuc-02' #@param {type:"string"}\nworkDir = Google_Drive_Path\nJobname = "mNG-flex-NLuc" #@param {type: "string"}\n\nCoarse_grained_model = "Martini3" #@param ["Martini", "Martini3"]\n\nbatch_size = 1 #@param {type: "number"}\n#@markdown - Batch size should be a divisor of the total number of frames.\n# device = "cuda" #@param ["cpu", "cuda"]\n\ntraj_input = os.path.join(workDir, str(Jobname) + "_cg_nw.dcd")\npdb_input = os.path.join(workDir, str(Jobname) + "_nw.pdb")\npdb_ini_output = os.path.join(workDir, str(Jobname) + "_frame0_backmapped.pdb")\ntraj_output = os.path.join(workDir, str(Jobname) + "_backmapped.dcd")\npdb_output = os.path.join(workDir, str(Jobname) + "_backmapped.pdb")\nbackmap_align_dcd = os.path.join(workDir, str(Jobname) + "_backmapped_align.dcd")\nbackmap_align_pdb = os.path.join(workDir, str(Jobname) + "_backmapped_align.pdb")\n\nsubprocess.run("convert_cg2all -p " + str(pdb_input) + " -o " + str(pdb_ini_output) + " --cg " + str(Coarse_grained_model), shell=True)\nsubprocess.run("convert_cg2all -p " + ...

[pablo-arantes]

Hi @kabirbiswas

Thank you for letting me know about the issue.
I will check and back to you.

Best,

Pablo