search

pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
MIT License
377 stars 97 forks source link

Martini+cg2all.ipynb | Parameters to generate the Martini topology #108

Open sflores14 opened 2 months ago

sflores14 commented 2 months ago

Hello, I encountered the following error when trying to generate topology using Martinize3001 and Martini22. 

FileNotFoundError                         Traceback (most recent call last)
<ipython-input-15-d932e83f8062> in <cell line: 79>()
     77 os.system("insane -o " + str(gro_martini) + " -p " + str(top_temp) + " -f "  + str(pdb_nw_martini) + " -d " + str(size_box) + " -sol W -salt " + str(Concentration) + " -charge auto -pbc " + str(box_type))
     78 
---> 79 with open(top_martini, 'r') as f:
     80     lines = f.readlines()
     81 # Remove the first line

FileNotFoundError: [Errno 2] No such file or directory: '/content/drive/MyDrive/Colab_Simulations/MARTINI/martini.top'

Any help with getting past this step would be appreciated.

pablo-arantes commented 2 months ago

Hi @sflores14,

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

Best,

Thank you.